Query 042576
Match_columns 313
No_of_seqs 203 out of 555
Neff 5.8
Searched_HMMs 46136
Date Fri Mar 29 07:31:47 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/042576.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/042576hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2648 Diphthamide biosynthes 100.0 4.8E-81 1E-85 608.7 27.2 286 1-295 113-406 (453)
2 TIGR00322 diphth2_R diphthamid 100.0 1.8E-74 3.8E-79 555.5 29.3 240 1-247 82-323 (332)
3 TIGR03682 arCOG04112 arCOG0411 100.0 1.6E-70 3.4E-75 523.5 28.1 234 1-241 63-298 (308)
4 PF01866 Diphthamide_syn: Puta 100.0 6.4E-71 1.4E-75 525.7 20.1 241 1-247 56-300 (307)
5 TIGR00272 DPH2 diphthamide bio 100.0 1.4E-62 3.1E-67 493.5 27.3 245 1-249 117-376 (496)
6 COG1736 DPH2 Diphthamide synth 100.0 1.8E-62 3.8E-67 471.2 26.6 256 1-292 86-345 (347)
7 COG1609 PurR Transcriptional r 90.0 8.3 0.00018 37.2 13.6 151 39-195 60-219 (333)
8 PF00532 Peripla_BP_1: Peripla 85.7 29 0.00064 32.3 14.1 155 48-211 16-186 (279)
9 PRK09492 treR trehalose repres 82.6 5 0.00011 37.2 7.4 78 152-230 61-143 (315)
10 cd01537 PBP1_Repressors_Sugar_ 81.9 34 0.00073 29.8 12.5 130 48-183 14-148 (264)
11 cd06320 PBP1_allose_binding Pe 80.0 45 0.00097 29.9 14.6 159 48-210 14-187 (275)
12 PRK07188 nicotinate phosphorib 78.1 6.8 0.00015 38.8 6.9 65 145-209 219-307 (352)
13 cd01574 PBP1_LacI Ligand-bindi 74.4 42 0.00091 29.8 10.6 143 47-196 13-159 (264)
14 cd06280 PBP1_LacI_like_4 Ligan 72.2 14 0.0003 33.1 7.0 60 155-215 1-65 (263)
15 cd06289 PBP1_MalI_like Ligand- 71.7 10 0.00022 33.7 5.9 76 155-231 1-84 (268)
16 cd06313 PBP1_ABC_sugar_binding 71.7 78 0.0017 28.6 12.1 146 47-196 13-167 (272)
17 TIGR02417 fruct_sucro_rep D-fr 71.4 44 0.00095 31.1 10.4 151 39-195 62-220 (327)
18 cd06287 PBP1_LacI_like_8 Ligan 70.6 85 0.0018 28.6 14.1 127 47-187 21-152 (269)
19 TIGR02990 ectoine_eutA ectoine 70.5 11 0.00024 35.2 6.0 82 148-236 116-216 (239)
20 PRK05569 flavodoxin; Provision 70.4 23 0.00051 29.2 7.5 56 155-216 3-58 (141)
21 cd06270 PBP1_GalS_like Ligand 70.3 80 0.0017 28.2 12.8 144 47-196 13-161 (268)
22 cd01536 PBP1_ABC_sugar_binding 70.1 8.9 0.00019 33.8 5.1 60 155-215 1-65 (267)
23 cd06301 PBP1_rhizopine_binding 69.4 83 0.0018 28.0 13.6 133 47-183 13-153 (272)
24 cd06274 PBP1_FruR Ligand bindi 68.9 16 0.00034 32.7 6.5 61 155-216 1-66 (264)
25 PLN02925 4-hydroxy-3-methylbut 68.8 57 0.0012 35.3 11.4 144 21-196 107-278 (733)
26 cd06277 PBP1_LacI_like_1 Ligan 68.5 17 0.00038 32.5 6.7 61 156-217 2-70 (268)
27 cd06273 PBP1_GntR_like_1 This 68.5 86 0.0019 27.8 12.0 157 47-213 13-186 (268)
28 PF00731 AIRC: AIR carboxylase 68.1 20 0.00044 31.3 6.7 56 155-213 2-63 (150)
29 COG0041 PurE Phosphoribosylcar 67.9 20 0.00043 31.7 6.6 46 155-203 4-50 (162)
30 TIGR02405 trehalos_R_Ecol treh 67.7 28 0.00061 32.4 8.2 63 152-215 58-125 (311)
31 PRK06703 flavodoxin; Provision 67.4 21 0.00045 30.1 6.6 55 155-215 3-57 (151)
32 TIGR01753 flav_short flavodoxi 67.0 22 0.00048 28.9 6.6 55 156-216 1-55 (140)
33 cd06293 PBP1_LacI_like_11 Liga 66.8 21 0.00045 32.0 6.9 61 155-216 1-66 (269)
34 PRK00694 4-hydroxy-3-methylbut 66.8 70 0.0015 33.9 11.3 145 21-197 42-214 (606)
35 cd06354 PBP1_BmpA_PnrA_like Pe 65.9 84 0.0018 28.5 10.8 129 47-183 16-150 (265)
36 cd06298 PBP1_CcpA_like Ligand- 65.8 15 0.00032 32.7 5.7 60 155-215 1-65 (268)
37 cd06298 PBP1_CcpA_like Ligand- 65.8 55 0.0012 29.0 9.4 130 47-186 13-150 (268)
38 PRK01045 ispH 4-hydroxy-3-meth 65.1 70 0.0015 31.0 10.4 119 36-183 154-283 (298)
39 cd06279 PBP1_LacI_like_3 Ligan 64.9 14 0.00031 33.7 5.5 62 155-217 1-68 (283)
40 cd06272 PBP1_hexuronate_repres 64.7 15 0.00032 32.8 5.5 59 155-215 1-61 (261)
41 cd06271 PBP1_AglR_RafR_like Li 64.6 21 0.00046 31.6 6.4 60 156-215 2-69 (268)
42 cd01542 PBP1_TreR_like Ligand- 64.5 14 0.00029 32.9 5.2 60 155-215 1-65 (259)
43 cd06273 PBP1_GntR_like_1 This 64.0 15 0.00034 32.7 5.5 77 155-232 1-84 (268)
44 PRK10014 DNA-binding transcrip 63.9 23 0.00051 33.1 6.9 79 152-231 63-149 (342)
45 PRK15408 autoinducer 2-binding 63.5 1.4E+02 0.0031 28.7 12.6 176 36-215 22-219 (336)
46 PRK05568 flavodoxin; Provision 63.3 40 0.00087 27.8 7.5 56 155-216 3-58 (142)
47 cd06278 PBP1_LacI_like_2 Ligan 63.3 1.1E+02 0.0023 27.0 12.0 140 47-196 13-158 (266)
48 cd06270 PBP1_GalS_like Ligand 63.2 26 0.00056 31.3 6.8 60 155-215 1-65 (268)
49 PF04392 ABC_sub_bind: ABC tra 62.7 14 0.00029 34.8 5.0 103 137-240 115-225 (294)
50 cd06310 PBP1_ABC_sugar_binding 62.6 12 0.00025 33.7 4.4 62 155-216 1-68 (273)
51 cd01545 PBP1_SalR Ligand-bindi 62.5 32 0.00069 30.6 7.2 60 155-214 1-65 (270)
52 COG1609 PurR Transcriptional r 62.5 42 0.00092 32.3 8.5 61 152-213 57-122 (333)
53 PF00885 DMRL_synthase: 6,7-di 62.1 24 0.00051 30.5 6.0 87 153-240 3-117 (144)
54 PRK12360 4-hydroxy-3-methylbut 62.0 70 0.0015 30.7 9.7 114 37-181 156-280 (281)
55 cd01542 PBP1_TreR_like Ligand- 61.4 94 0.002 27.4 10.1 129 47-184 13-146 (259)
56 PRK11303 DNA-binding transcrip 60.6 40 0.00086 31.4 7.8 63 152-215 60-127 (328)
57 cd06295 PBP1_CelR Ligand bindi 59.0 35 0.00076 30.6 6.9 64 152-215 2-74 (275)
58 COG2984 ABC-type uncharacteriz 58.7 39 0.00085 33.1 7.4 196 37-239 30-252 (322)
59 cd06283 PBP1_RegR_EndR_KdgR_li 58.6 29 0.00063 30.7 6.2 59 155-214 1-64 (267)
60 PRK14987 gluconate operon tran 58.2 31 0.00067 32.2 6.6 63 152-215 62-129 (331)
61 cd01574 PBP1_LacI Ligand-bindi 58.0 32 0.00069 30.5 6.4 61 155-215 1-66 (264)
62 cd06309 PBP1_YtfQ_like Peripla 57.7 1.4E+02 0.0031 26.7 10.8 134 45-183 11-154 (273)
63 PRK09526 lacI lac repressor; R 57.4 61 0.0013 30.3 8.5 61 152-212 62-127 (342)
64 cd06276 PBP1_FucR_like Ligand- 57.2 1.2E+02 0.0026 27.3 10.1 132 47-187 12-150 (247)
65 TIGR02417 fruct_sucro_rep D-fr 57.2 64 0.0014 30.0 8.6 62 152-214 59-125 (327)
66 cd06281 PBP1_LacI_like_5 Ligan 57.0 39 0.00084 30.3 6.8 60 155-215 1-65 (269)
67 PRK11041 DNA-binding transcrip 56.8 59 0.0013 29.8 8.1 62 152-214 34-100 (309)
68 cd06315 PBP1_ABC_sugar_binding 56.7 38 0.00083 30.9 6.8 61 154-215 1-66 (280)
69 cd06316 PBP1_ABC_sugar_binding 56.6 19 0.0004 33.1 4.7 61 155-215 1-66 (294)
70 PRK07308 flavodoxin; Validated 56.3 51 0.0011 27.5 7.0 57 155-217 3-59 (146)
71 cd06299 PBP1_LacI_like_13 Liga 56.2 37 0.00081 30.1 6.5 60 155-215 1-65 (265)
72 PRK10423 transcriptional repre 55.8 60 0.0013 30.0 8.1 62 152-214 55-121 (327)
73 PF00532 Peripla_BP_1: Peripla 55.8 38 0.00081 31.6 6.7 61 154-215 2-66 (279)
74 PRK02048 4-hydroxy-3-methylbut 55.1 1.3E+02 0.0028 32.1 11.0 141 21-193 38-206 (611)
75 COG5623 CLP1 Predicted GTPase 54.7 67 0.0015 31.8 8.2 169 21-200 82-266 (424)
76 cd06291 PBP1_Qymf_like Ligand 53.9 39 0.00084 30.1 6.3 60 155-215 1-65 (265)
77 PRK00087 4-hydroxy-3-methylbut 53.8 1.1E+02 0.0024 32.6 10.5 118 34-182 150-278 (647)
78 PRK10703 DNA-binding transcrip 53.8 31 0.00068 32.3 5.9 62 152-214 58-124 (341)
79 PRK05723 flavodoxin; Provision 53.7 51 0.0011 28.4 6.7 55 155-215 2-56 (151)
80 PF00919 UPF0004: Uncharacteri 53.7 44 0.00095 26.8 5.9 64 146-210 31-97 (98)
81 PF00258 Flavodoxin_1: Flavodo 53.5 33 0.00071 28.2 5.4 54 158-215 1-54 (143)
82 PF06180 CbiK: Cobalt chelatas 53.2 1.9E+02 0.0042 27.4 11.0 15 93-107 141-155 (262)
83 PRK11303 DNA-binding transcrip 53.1 1.9E+02 0.0041 26.7 12.9 148 39-195 63-221 (328)
84 PRK09526 lacI lac repressor; R 51.9 2E+02 0.0044 26.7 13.6 150 39-196 65-224 (342)
85 cd06286 PBP1_CcpB_like Ligand- 51.7 60 0.0013 28.8 7.1 60 155-215 1-65 (260)
86 cd06284 PBP1_LacI_like_6 Ligan 51.6 56 0.0012 28.8 6.9 58 156-214 2-64 (267)
87 cd06294 PBP1_ycjW_transcriptio 51.5 1.7E+02 0.0037 25.8 12.0 131 47-184 18-153 (270)
88 TIGR01162 purE phosphoribosyla 51.4 46 0.00099 29.4 6.0 55 156-213 1-61 (156)
89 cd06267 PBP1_LacI_sugar_bindin 51.4 1.6E+02 0.0035 25.5 13.0 34 152-185 115-148 (264)
90 cd06275 PBP1_PurR Ligand-bindi 51.2 61 0.0013 28.8 7.1 60 155-215 1-65 (269)
91 cd06296 PBP1_CatR_like Ligand- 50.9 54 0.0012 29.1 6.7 34 156-189 2-35 (270)
92 cd06282 PBP1_GntR_like_2 Ligan 50.6 41 0.00089 29.7 5.9 32 156-187 2-33 (266)
93 cd06290 PBP1_LacI_like_9 Ligan 50.5 44 0.00095 29.7 6.0 60 155-215 1-65 (265)
94 PRK10653 D-ribose transporter 50.4 41 0.00089 30.9 6.0 62 152-214 25-91 (295)
95 cd01538 PBP1_ABC_xylose_bindin 50.3 27 0.00059 32.0 4.8 30 156-185 2-31 (288)
96 cd06284 PBP1_LacI_like_6 Ligan 50.0 1.8E+02 0.0039 25.6 12.2 45 152-196 114-160 (267)
97 COG0716 FldA Flavodoxins [Ener 48.9 64 0.0014 27.3 6.5 59 154-217 2-60 (151)
98 cd06292 PBP1_LacI_like_10 Liga 48.9 44 0.00095 29.9 5.8 59 155-214 1-64 (273)
99 cd06302 PBP1_LsrB_Quorum_Sensi 48.3 44 0.00095 30.9 5.8 59 155-213 1-64 (298)
100 PRK05282 (alpha)-aspartyl dipe 48.2 65 0.0014 30.0 6.9 45 23-67 17-65 (233)
101 cd06278 PBP1_LacI_like_2 Ligan 48.1 62 0.0013 28.5 6.6 34 156-189 2-35 (266)
102 cd06325 PBP1_ABC_uncharacteriz 47.9 1.7E+02 0.0037 26.1 9.5 36 152-188 130-165 (281)
103 cd01452 VWA_26S_proteasome_sub 47.0 60 0.0013 29.2 6.3 49 154-203 108-158 (187)
104 COG1832 Predicted CoA-binding 46.8 28 0.0006 30.2 3.8 95 29-125 8-109 (140)
105 TIGR03705 poly_P_kin polyphosp 46.3 4.2E+02 0.0091 28.7 14.2 92 95-190 442-554 (672)
106 PRK09004 FMN-binding protein M 46.3 64 0.0014 27.5 6.1 53 154-213 2-54 (146)
107 cd01575 PBP1_GntR Ligand-bindi 46.3 56 0.0012 28.9 6.0 60 155-215 1-65 (268)
108 TIGR00216 ispH_lytB (E)-4-hydr 46.2 2.1E+02 0.0045 27.5 10.1 117 34-181 150-279 (280)
109 cd06297 PBP1_LacI_like_12 Liga 45.7 39 0.00085 30.4 5.0 60 156-215 2-65 (269)
110 cd06290 PBP1_LacI_like_9 Ligan 45.5 2.1E+02 0.0046 25.2 9.7 131 47-186 13-148 (265)
111 TIGR01007 eps_fam capsular exo 45.4 68 0.0015 28.1 6.4 56 139-196 4-59 (204)
112 cd06293 PBP1_LacI_like_11 Liga 45.3 2.2E+02 0.0048 25.2 12.1 130 47-185 13-148 (269)
113 PF02401 LYTB: LytB protein; 45.1 1.4E+02 0.0029 28.8 8.7 119 34-181 151-280 (281)
114 cd06294 PBP1_ycjW_transcriptio 44.9 45 0.00098 29.6 5.2 32 156-187 2-38 (270)
115 PLN02404 6,7-dimethyl-8-ribity 44.7 76 0.0016 27.5 6.3 87 153-240 7-121 (141)
116 cd01536 PBP1_ABC_sugar_binding 44.5 2.1E+02 0.0046 24.9 14.5 146 47-196 13-165 (267)
117 TIGR00640 acid_CoA_mut_C methy 44.3 60 0.0013 27.4 5.6 71 145-217 45-117 (132)
118 COG1111 MPH1 ERCC4-like helica 44.1 89 0.0019 32.7 7.6 47 23-71 350-401 (542)
119 PF02514 CobN-Mg_chel: CobN/Ma 44.1 34 0.00074 38.9 5.1 94 152-248 70-178 (1098)
120 PRK09271 flavodoxin; Provision 43.6 80 0.0017 27.0 6.4 58 155-215 2-60 (160)
121 cd06316 PBP1_ABC_sugar_binding 43.5 2.6E+02 0.0055 25.5 13.9 41 143-184 117-157 (294)
122 cd06305 PBP1_methylthioribose_ 43.3 68 0.0015 28.6 6.1 33 156-188 2-34 (273)
123 PRK10423 transcriptional repre 43.1 2.3E+02 0.005 26.1 9.9 138 39-186 58-207 (327)
124 PRK05443 polyphosphate kinase; 43.0 4.7E+02 0.01 28.4 17.4 92 95-190 451-563 (691)
125 PRK14571 D-alanyl-alanine synt 43.0 88 0.0019 29.3 7.1 60 155-216 2-63 (299)
126 cd06285 PBP1_LacI_like_7 Ligan 42.8 1E+02 0.0022 27.3 7.3 60 155-215 1-65 (265)
127 PRK10355 xylF D-xylose transpo 42.8 78 0.0017 30.2 6.8 63 152-215 24-91 (330)
128 cd05569 PTS_IIB_fructose PTS_I 42.7 1E+02 0.0022 24.4 6.3 68 156-230 2-76 (96)
129 PRK00061 ribH 6,7-dimethyl-8-r 42.5 66 0.0014 28.1 5.7 86 153-239 12-125 (154)
130 PRK10703 DNA-binding transcrip 42.4 2.9E+02 0.0062 25.7 11.9 163 39-212 61-246 (341)
131 cd06304 PBP1_BmpA_like Peripla 42.4 2.5E+02 0.0055 25.1 13.2 131 47-187 15-153 (260)
132 TIGR01752 flav_long flavodoxin 42.3 59 0.0013 28.1 5.3 49 19-67 60-115 (167)
133 cd06307 PBP1_uncharacterized_s 42.1 39 0.00084 30.4 4.4 33 156-188 2-34 (275)
134 cd06285 PBP1_LacI_like_7 Ligan 42.1 2.5E+02 0.0053 24.9 12.3 131 47-186 13-147 (265)
135 cd06277 PBP1_LacI_like_1 Ligan 41.8 2.4E+02 0.0051 25.1 9.5 132 47-186 16-151 (268)
136 cd06288 PBP1_sucrose_transcrip 41.6 1E+02 0.0022 27.3 7.0 60 155-215 1-66 (269)
137 COG2185 Sbm Methylmalonyl-CoA 41.4 59 0.0013 28.3 5.1 57 145-203 55-112 (143)
138 cd01537 PBP1_Repressors_Sugar_ 41.4 83 0.0018 27.2 6.3 30 156-185 2-31 (264)
139 cd06312 PBP1_ABC_sugar_binding 41.2 71 0.0015 28.7 6.0 60 155-214 1-66 (271)
140 cd05013 SIS_RpiR RpiR-like pro 41.1 1.7E+02 0.0038 23.0 7.7 68 145-218 6-73 (139)
141 cd06286 PBP1_CcpB_like Ligand- 41.0 2.3E+02 0.0049 25.0 9.2 129 48-186 14-147 (260)
142 TIGR01481 ccpA catabolite cont 40.7 1.6E+02 0.0036 27.2 8.5 63 152-215 58-125 (329)
143 TIGR00147 lipid kinase, YegS/R 40.4 1.2E+02 0.0027 28.2 7.6 40 154-193 2-42 (293)
144 PF03698 UPF0180: Uncharacteri 40.3 56 0.0012 25.7 4.3 40 49-103 7-46 (80)
145 cd06288 PBP1_sucrose_transcrip 40.3 2.6E+02 0.0056 24.6 11.2 61 152-213 115-185 (269)
146 COG0529 CysC Adenylylsulfate k 39.9 73 0.0016 29.1 5.6 39 152-190 20-58 (197)
147 cd06296 PBP1_CatR_like Ligand- 39.9 2.7E+02 0.0057 24.6 11.5 128 48-186 14-150 (270)
148 PF03358 FMN_red: NADPH-depend 39.8 63 0.0014 26.8 5.0 40 155-194 2-42 (152)
149 cd01541 PBP1_AraR Ligand-bindi 39.7 1.1E+02 0.0023 27.4 6.8 31 156-186 2-32 (273)
150 PRK06455 riboflavin synthase; 39.6 1.1E+02 0.0024 26.9 6.6 58 154-215 2-66 (155)
151 cd06304 PBP1_BmpA_like Peripla 39.3 78 0.0017 28.5 5.9 34 155-188 1-36 (260)
152 cd06320 PBP1_allose_binding Pe 39.2 58 0.0012 29.2 5.0 30 156-185 2-31 (275)
153 cd06299 PBP1_LacI_like_13 Liga 39.2 2.7E+02 0.0058 24.5 10.1 64 152-215 115-185 (265)
154 PRK10310 PTS system galactitol 39.1 1E+02 0.0022 24.4 5.8 53 158-213 6-58 (94)
155 cd06318 PBP1_ABC_sugar_binding 39.0 62 0.0013 29.1 5.2 60 155-215 1-65 (282)
156 PF01583 APS_kinase: Adenylyls 39.0 72 0.0016 27.9 5.3 36 156-191 3-38 (156)
157 cd06295 PBP1_CelR Ligand bindi 38.6 2.9E+02 0.0062 24.6 12.6 155 48-214 25-195 (275)
158 cd06289 PBP1_MalI_like Ligand- 38.4 2.8E+02 0.006 24.4 11.8 33 152-184 116-148 (268)
159 cd01540 PBP1_arabinose_binding 38.3 69 0.0015 28.9 5.4 58 155-214 1-63 (289)
160 cd04502 SGNH_hydrolase_like_7 37.8 94 0.002 26.1 5.9 24 139-163 38-61 (171)
161 PRK08662 nicotinate phosphorib 37.7 69 0.0015 31.6 5.6 56 154-209 227-285 (343)
162 PRK06756 flavodoxin; Provision 37.7 98 0.0021 25.8 5.9 47 22-68 68-119 (148)
163 cd02071 MM_CoA_mut_B12_BD meth 37.6 1.6E+02 0.0034 24.1 7.0 62 152-216 50-113 (122)
164 cd06308 PBP1_sensor_kinase_lik 37.4 95 0.0021 27.7 6.1 34 155-188 1-35 (270)
165 PRK12359 flavodoxin FldB; Prov 37.4 1.2E+02 0.0025 26.9 6.5 53 155-216 2-55 (172)
166 PF02012 BNR: BNR/Asp-box repe 37.3 18 0.00039 18.6 0.8 10 282-291 1-11 (12)
167 COG1797 CobB Cobyrinic acid a, 37.2 1.5E+02 0.0032 30.6 7.8 75 18-105 212-300 (451)
168 cd01543 PBP1_XylR Ligand-bindi 37.1 59 0.0013 29.1 4.8 56 155-213 1-58 (265)
169 PRK10727 DNA-binding transcrip 37.0 2.1E+02 0.0045 26.9 8.6 62 152-214 58-124 (343)
170 PF00781 DAGK_cat: Diacylglyce 36.8 1.2E+02 0.0026 24.7 6.2 40 155-195 1-40 (130)
171 PF02302 PTS_IIB: PTS system, 36.7 1.3E+02 0.0027 22.7 5.9 55 158-218 3-58 (90)
172 PRK06756 flavodoxin; Provision 36.6 1.5E+02 0.0032 24.7 6.8 55 155-215 3-58 (148)
173 cd06300 PBP1_ABC_sugar_binding 36.2 1E+02 0.0022 27.5 6.2 60 155-214 1-69 (272)
174 PRK08105 flavodoxin; Provision 36.1 95 0.0021 26.5 5.6 41 154-195 2-42 (149)
175 cd06271 PBP1_AglR_RafR_like Li 35.9 3E+02 0.0065 24.1 15.5 159 46-213 16-189 (268)
176 PLN02349 glycerol-3-phosphate 35.2 89 0.0019 31.7 5.9 153 20-186 162-339 (426)
177 cd02042 ParA ParA and ParB of 35.1 1.4E+02 0.0031 22.8 6.1 48 158-217 3-50 (104)
178 PRK10401 DNA-binding transcrip 34.5 2.3E+02 0.005 26.6 8.5 62 152-214 58-124 (346)
179 cd06319 PBP1_ABC_sugar_binding 34.5 84 0.0018 28.0 5.3 32 156-187 2-33 (277)
180 PRK15395 methyl-galactoside AB 34.2 1.5E+02 0.0033 28.1 7.2 64 152-215 23-91 (330)
181 cd06274 PBP1_FruR Ligand bindi 34.1 3.3E+02 0.0072 24.0 14.7 130 47-185 13-148 (264)
182 PF01408 GFO_IDH_MocA: Oxidore 34.0 2.3E+02 0.005 22.1 8.2 89 96-187 3-117 (120)
183 PRK10339 DNA-binding transcrip 33.7 76 0.0016 29.6 5.0 58 152-214 62-123 (327)
184 PF01729 QRPTase_C: Quinolinat 33.5 78 0.0017 28.0 4.7 82 119-213 74-156 (169)
185 cd01391 Periplasmic_Binding_Pr 33.5 3E+02 0.0064 23.3 12.8 39 152-191 123-161 (269)
186 PRK09701 D-allose transporter 33.3 1.3E+02 0.0027 28.2 6.5 62 152-213 23-90 (311)
187 cd01545 PBP1_SalR Ligand-bindi 33.2 3.4E+02 0.0073 23.9 12.3 35 152-186 117-151 (270)
188 TIGR01754 flav_RNR ribonucleot 33.0 82 0.0018 26.2 4.7 57 155-215 2-59 (140)
189 TIGR01205 D_ala_D_alaTIGR D-al 32.9 1.6E+02 0.0034 27.6 7.0 58 155-213 1-71 (315)
190 COG0279 GmhA Phosphoheptose is 32.7 2.3E+02 0.0049 25.5 7.4 103 93-210 54-160 (176)
191 TIGR00114 lumazine-synth 6,7-d 32.5 1.4E+02 0.0029 25.7 5.9 85 155-240 2-114 (138)
192 PRK09426 methylmalonyl-CoA mut 32.5 1E+02 0.0022 33.6 6.2 72 145-219 625-699 (714)
193 PF09547 Spore_IV_A: Stage IV 32.5 72 0.0016 32.9 4.8 71 152-223 143-226 (492)
194 TIGR03018 pepcterm_TyrKin exop 32.1 2E+02 0.0044 25.4 7.3 61 135-195 12-77 (207)
195 cd01571 NAPRTase_B Nicotinate 32.0 66 0.0014 31.0 4.4 56 154-209 211-270 (302)
196 cd06267 PBP1_LacI_sugar_bindin 31.9 90 0.002 27.1 5.0 25 171-196 44-68 (264)
197 PRK02910 light-independent pro 31.8 1.1E+02 0.0024 31.6 6.3 76 153-231 158-238 (519)
198 TIGR02955 TMAO_TorT TMAO reduc 31.6 1.1E+02 0.0024 28.1 5.7 36 156-191 2-37 (295)
199 PRK05319 rplD 50S ribosomal pr 31.6 3.5E+02 0.0076 24.6 8.8 115 72-208 49-173 (205)
200 TIGR03449 mycothiol_MshA UDP-N 31.6 1.5E+02 0.0033 28.3 6.9 59 155-214 253-311 (405)
201 PRK11914 diacylglycerol kinase 31.6 1.8E+02 0.0038 27.5 7.2 39 154-192 9-48 (306)
202 PLN02949 transferase, transfer 31.1 80 0.0017 32.1 5.0 72 156-238 305-377 (463)
203 cd06323 PBP1_ribose_binding Pe 31.1 3.6E+02 0.0079 23.6 11.1 137 47-187 13-156 (268)
204 COG2984 ABC-type uncharacteriz 31.1 1.4E+02 0.003 29.4 6.3 48 21-68 143-193 (322)
205 TIGR03029 EpsG chain length de 31.1 3.3E+02 0.0072 25.0 8.8 56 137-192 86-141 (274)
206 cd02036 MinD Bacterial cell di 31.0 88 0.0019 26.2 4.6 60 158-217 3-73 (179)
207 cd05565 PTS_IIB_lactose PTS_II 31.0 1.4E+02 0.0031 24.1 5.5 55 158-218 4-58 (99)
208 PRK10936 TMAO reductase system 30.8 1.2E+02 0.0027 28.8 6.0 65 149-214 43-113 (343)
209 PLN02948 phosphoribosylaminoim 30.8 1.6E+02 0.0034 31.0 7.3 98 111-212 354-472 (577)
210 TIGR00550 nadA quinolinate syn 30.7 5.1E+02 0.011 25.2 10.8 28 94-123 144-171 (310)
211 PF13964 Kelch_6: Kelch motif 30.7 51 0.0011 22.3 2.5 18 113-130 25-42 (50)
212 cd03821 GT1_Bme6_like This fam 30.5 1.3E+02 0.0027 27.2 5.8 54 178-231 254-310 (375)
213 cd02040 NifH NifH gene encodes 30.4 92 0.002 28.3 4.9 36 154-191 2-37 (270)
214 PRK14095 pgi glucose-6-phospha 29.7 2.9E+02 0.0062 29.1 8.8 50 152-203 202-256 (533)
215 TIGR01931 cysJ sulfite reducta 29.7 1.1E+02 0.0025 32.2 6.0 51 152-203 57-107 (597)
216 KOG3360 Acylphosphatase [Energ 29.6 1E+02 0.0022 25.2 4.3 56 140-196 22-83 (98)
217 COG0426 FpaA Uncharacterized f 29.3 4.8E+02 0.01 26.4 10.0 140 22-200 229-377 (388)
218 cd00300 LDH_like L-lactate deh 29.1 1.4E+02 0.0029 28.5 5.9 76 117-193 25-116 (300)
219 PRK11104 hemG protoporphyrinog 29.0 1.1E+02 0.0023 26.9 4.9 54 155-215 2-55 (177)
220 PRK13055 putative lipid kinase 28.9 2.4E+02 0.0052 27.2 7.7 38 154-191 3-41 (334)
221 cd06354 PBP1_BmpA_PnrA_like Pe 28.9 1.5E+02 0.0033 26.8 6.0 14 170-183 19-32 (265)
222 cd06325 PBP1_ABC_uncharacteriz 28.3 1.6E+02 0.0035 26.2 6.1 58 155-215 1-70 (281)
223 PRK10401 DNA-binding transcrip 28.3 5E+02 0.011 24.3 12.5 140 39-186 61-209 (346)
224 PF02593 dTMP_synthase: Thymid 28.2 94 0.002 28.8 4.5 41 143-186 66-106 (217)
225 cd06317 PBP1_ABC_sugar_binding 28.1 1.2E+02 0.0026 26.9 5.2 30 156-185 2-32 (275)
226 cd06321 PBP1_ABC_sugar_binding 27.6 1.7E+02 0.0037 26.0 6.1 30 156-185 2-31 (271)
227 PRK13185 chlL protochlorophyll 27.5 1.1E+02 0.0023 28.2 4.8 37 153-191 2-38 (270)
228 cd03466 Nitrogenase_NifN_2 Nit 27.3 6.4E+02 0.014 25.2 13.9 183 8-197 117-337 (429)
229 TIGR02363 dhaK1 dihydroxyaceto 27.3 1.8E+02 0.0039 28.7 6.4 45 152-196 251-298 (329)
230 PF01976 DUF116: Protein of un 27.2 60 0.0013 28.4 2.9 47 169-217 72-118 (158)
231 cd03798 GT1_wlbH_like This fam 27.2 41 0.00089 30.2 2.0 60 173-232 246-308 (377)
232 PF09861 DUF2088: Domain of un 27.1 97 0.0021 28.2 4.3 35 148-184 50-86 (204)
233 cd01538 PBP1_ABC_xylose_bindin 27.0 4.7E+02 0.01 23.7 9.1 129 47-183 13-155 (288)
234 TIGR01752 flav_long flavodoxin 26.9 1.7E+02 0.0036 25.2 5.7 53 155-215 1-53 (167)
235 cd01540 PBP1_arabinose_binding 26.9 4.6E+02 0.01 23.4 9.3 135 48-186 14-163 (289)
236 cd06319 PBP1_ABC_sugar_binding 26.5 4.5E+02 0.0098 23.2 12.1 59 153-212 125-192 (277)
237 KOG2892 Porphobilinogen deamin 26.4 3.3E+02 0.0072 26.5 7.9 78 21-101 20-115 (320)
238 cd03819 GT1_WavL_like This fam 26.3 1.6E+02 0.0034 27.1 5.8 41 154-195 185-226 (355)
239 cd01981 Pchlide_reductase_B Pc 26.3 1E+02 0.0022 30.7 4.8 79 152-232 161-243 (430)
240 TIGR01481 ccpA catabolite cont 26.2 5.2E+02 0.011 23.8 12.5 139 39-186 61-210 (329)
241 PF01656 CbiA: CobQ/CobB/MinD/ 26.1 2E+02 0.0042 24.3 6.0 41 158-198 2-42 (195)
242 PF13407 Peripla_BP_4: Peripla 25.9 2.2E+02 0.0048 25.1 6.5 43 156-198 1-43 (257)
243 cd06310 PBP1_ABC_sugar_binding 25.9 4.6E+02 0.01 23.1 11.6 136 48-187 14-158 (273)
244 cd00133 PTS_IIB PTS_IIB: subun 25.6 2.5E+02 0.0054 20.0 5.8 50 158-211 3-52 (84)
245 PRK12419 riboflavin synthase s 25.6 2E+02 0.0042 25.5 5.8 85 154-239 11-123 (158)
246 PF00205 TPP_enzyme_M: Thiamin 25.6 68 0.0015 26.3 2.9 68 145-216 4-88 (137)
247 cd01544 PBP1_GalR Ligand-bindi 25.5 4.8E+02 0.01 23.2 14.2 135 46-196 17-161 (270)
248 cd06318 PBP1_ABC_sugar_binding 25.5 4.8E+02 0.01 23.2 12.8 134 47-184 13-154 (282)
249 cd06301 PBP1_rhizopine_binding 25.5 1.6E+02 0.0036 26.1 5.6 8 182-189 55-62 (272)
250 cd03801 GT1_YqgM_like This fam 25.4 1.3E+02 0.0027 26.8 4.8 60 172-231 242-304 (374)
251 PRK14733 coaE dephospho-CoA ki 25.4 92 0.002 28.3 3.9 50 167-217 91-140 (204)
252 TIGR02990 ectoine_eutA ectoine 25.2 2.8E+02 0.006 25.8 7.1 30 37-68 120-150 (239)
253 PRK03980 flap endonuclease-1; 25.1 1.7E+02 0.0037 28.1 5.8 110 104-217 15-137 (292)
254 COG4152 ABC-type uncharacteriz 24.9 6.5E+02 0.014 24.4 9.5 29 180-210 219-247 (300)
255 cd01983 Fer4_NifH The Fer4_Nif 24.9 1.7E+02 0.0036 21.2 4.7 33 158-190 2-34 (99)
256 PRK09267 flavodoxin FldA; Vali 24.8 1.7E+02 0.0037 24.9 5.4 53 155-215 3-55 (169)
257 TIGR02634 xylF D-xylose ABC tr 24.6 1.6E+02 0.0035 27.3 5.5 28 157-184 2-29 (302)
258 TIGR01579 MiaB-like-C MiaB-lik 24.5 1.9E+02 0.004 28.8 6.2 30 180-210 60-92 (414)
259 PRK14481 dihydroxyacetone kina 24.5 2.1E+02 0.0046 28.2 6.4 45 152-196 250-297 (331)
260 COG1794 RacX Aspartate racemas 24.4 1.5E+02 0.0033 27.8 5.1 34 37-71 117-150 (230)
261 cd02117 NifH_like This family 24.4 1.4E+02 0.0031 26.4 4.9 33 155-189 2-34 (212)
262 PRK11041 DNA-binding transcrip 24.3 5.4E+02 0.012 23.3 11.4 141 38-186 36-185 (309)
263 cd03813 GT1_like_3 This family 24.1 1.8E+02 0.0038 29.3 6.0 56 154-214 324-379 (475)
264 cd01473 vWA_CTRP CTRP for CS 24.0 2.5E+02 0.0054 24.8 6.4 51 152-203 107-159 (192)
265 cd06323 PBP1_ribose_binding Pe 23.7 1.2E+02 0.0025 26.8 4.2 28 156-183 2-29 (268)
266 TIGR02014 BchZ chlorophyllide 23.7 1.4E+02 0.0031 30.6 5.3 77 152-230 151-227 (468)
267 cd01539 PBP1_GGBP Periplasmic 23.6 1.5E+02 0.0033 27.4 5.1 26 156-181 2-27 (303)
268 cd05566 PTS_IIB_galactitol PTS 23.4 2.2E+02 0.0048 21.5 5.2 54 158-215 4-57 (89)
269 PF09314 DUF1972: Domain of un 23.2 1.4E+02 0.003 26.9 4.5 58 158-217 5-66 (185)
270 cd06275 PBP1_PurR Ligand-bindi 23.0 5.2E+02 0.011 22.7 10.0 128 48-186 14-150 (269)
271 PRK14483 DhaKLM operon coactiv 23.0 2.3E+02 0.0051 27.9 6.4 45 152-196 250-297 (329)
272 PF06414 Zeta_toxin: Zeta toxi 22.8 2.6E+02 0.0057 24.5 6.3 50 139-192 79-128 (199)
273 PF13614 AAA_31: AAA domain; P 22.7 3.2E+02 0.007 22.3 6.5 46 158-203 4-49 (157)
274 KOG1184 Thiamine pyrophosphate 22.6 1.1E+02 0.0024 32.0 4.2 86 93-185 434-530 (561)
275 PF06564 YhjQ: YhjQ protein; 22.6 1.6E+02 0.0035 27.7 5.0 41 157-200 4-44 (243)
276 TIGR00550 nadA quinolinate syn 22.5 2E+02 0.0044 28.0 5.8 49 93-142 53-101 (310)
277 cd06292 PBP1_LacI_like_10 Liga 22.5 5.4E+02 0.012 22.7 12.7 130 47-185 13-154 (273)
278 cd06306 PBP1_TorT-like TorT-li 22.4 5.6E+02 0.012 22.8 15.6 158 47-210 13-189 (268)
279 cd01973 Nitrogenase_VFe_beta_l 22.4 8.3E+02 0.018 24.8 12.0 178 9-194 125-339 (454)
280 cd03825 GT1_wcfI_like This fam 22.4 2.6E+02 0.0057 25.6 6.5 56 155-211 2-57 (365)
281 TIGR02883 spore_cwlD N-acetylm 22.4 1.9E+02 0.0042 25.5 5.3 48 167-215 27-93 (189)
282 PRK03708 ppnK inorganic polyph 22.2 1.7E+02 0.0036 27.9 5.1 84 155-240 2-107 (277)
283 cd06314 PBP1_tmGBP Periplasmic 22.1 2.2E+02 0.0047 25.4 5.7 58 155-214 1-64 (271)
284 PRK08745 ribulose-phosphate 3- 22.1 4.4E+02 0.0095 24.3 7.7 41 171-211 157-198 (223)
285 PRK13232 nifH nitrogenase redu 22.0 1.6E+02 0.0034 27.2 4.9 34 154-189 2-35 (273)
286 TIGR01501 MthylAspMutase methy 22.0 1.9E+02 0.0041 24.7 4.9 46 145-193 44-90 (134)
287 cd06276 PBP1_FucR_like Ligand- 21.9 1.6E+02 0.0034 26.5 4.8 58 156-215 2-62 (247)
288 PF14157 YmzC: YmzC-like prote 21.8 50 0.0011 24.8 1.2 34 94-130 22-55 (63)
289 PRK08091 ribulose-phosphate 3- 21.8 4.3E+02 0.0092 24.6 7.6 49 163-211 153-206 (228)
290 PRK05452 anaerobic nitric oxid 21.8 3.9E+02 0.0086 27.4 8.1 79 152-237 250-331 (479)
291 TIGR00829 FRU PTS system, fruc 21.8 2.2E+02 0.0048 22.1 4.9 68 157-230 2-76 (85)
292 PF09652 Cas_VVA1548: Putative 21.7 3E+02 0.0065 22.3 5.6 49 158-214 37-93 (93)
293 TIGR02362 dhaK1b probable dihy 21.7 2.6E+02 0.0057 27.5 6.4 44 152-195 247-293 (326)
294 cd06322 PBP1_ABC_sugar_binding 21.4 1.8E+02 0.0039 25.7 5.0 32 156-187 2-33 (267)
295 PRK02649 ppnK inorganic polyph 21.4 1.9E+02 0.0042 27.9 5.4 36 154-190 2-37 (305)
296 PRK15408 autoinducer 2-binding 21.4 2.8E+02 0.006 26.7 6.6 63 152-214 22-89 (336)
297 cd03806 GT1_ALG11_like This fa 21.3 2E+02 0.0044 28.4 5.7 76 155-241 274-349 (419)
298 cd06300 PBP1_ABC_sugar_binding 21.3 5.8E+02 0.012 22.5 11.3 121 92-215 60-195 (272)
299 cd01543 PBP1_XylR Ligand-bindi 21.2 5.8E+02 0.013 22.5 12.2 127 46-186 11-141 (265)
300 PF01915 Glyco_hydro_3_C: Glyc 21.1 2E+02 0.0044 25.7 5.3 70 145-216 79-163 (227)
301 TIGR02955 TMAO_TorT TMAO reduc 21.1 6.4E+02 0.014 23.0 10.9 44 153-196 125-168 (295)
302 PRK10953 cysJ sulfite reductas 20.9 2.1E+02 0.0046 30.3 6.0 51 152-203 60-110 (600)
303 cd02034 CooC The accessory pro 20.8 2E+02 0.0044 23.4 4.7 36 158-193 2-37 (116)
304 TIGR01118 lacA galactose-6-pho 20.8 1.7E+02 0.0037 25.3 4.4 80 39-129 2-93 (141)
305 cd01481 vWA_collagen_alpha3-VI 20.8 4.1E+02 0.0088 22.8 6.9 49 152-203 105-153 (165)
306 PRK09240 thiH thiamine biosynt 20.7 2.3E+02 0.0049 28.0 5.9 57 139-197 201-263 (371)
307 cd06309 PBP1_YtfQ_like Peripla 20.7 1.9E+02 0.004 25.9 5.0 11 180-190 52-62 (273)
308 cd01982 Chlide_reductase_Z Chl 20.6 1.8E+02 0.004 29.3 5.3 74 153-228 155-228 (412)
309 TIGR02836 spore_IV_A stage IV 20.5 2E+02 0.0043 29.9 5.4 71 152-223 143-226 (492)
310 PRK13230 nitrogenase reductase 20.5 1.7E+02 0.0037 27.1 4.8 34 154-189 2-35 (279)
311 PRK11557 putative DNA-binding 20.5 3.2E+02 0.0068 25.2 6.6 64 145-216 121-186 (278)
312 cd03795 GT1_like_4 This family 20.4 87 0.0019 28.7 2.8 44 172-215 230-273 (357)
313 cd01575 PBP1_GntR Ligand-bindi 20.4 5.8E+02 0.013 22.2 16.4 158 47-214 13-186 (268)
314 CHL00175 minD septum-site dete 20.3 2E+02 0.0043 26.6 5.2 41 152-192 13-53 (281)
315 cd02037 MRP-like MRP (Multiple 20.3 1.7E+02 0.0036 24.8 4.3 35 158-192 3-37 (169)
316 PF07555 NAGidase: beta-N-acet 20.3 6.5E+02 0.014 24.4 8.8 88 106-196 20-117 (306)
317 PLN02204 diacylglycerol kinase 20.2 6.5E+02 0.014 27.0 9.3 64 148-213 155-226 (601)
318 PRK11468 dihydroxyacetone kina 20.2 2.4E+02 0.0052 28.2 5.8 45 152-196 274-321 (356)
319 PF08475 Baculo_VP91_N: Viral 20.1 89 0.0019 28.3 2.6 19 46-64 26-44 (183)
320 TIGR01278 DPOR_BchB light-inde 20.1 2.1E+02 0.0046 29.5 5.8 76 152-230 157-237 (511)
321 COG0761 lytB 4-Hydroxy-3-methy 20.1 8.2E+02 0.018 23.8 12.0 57 140-201 200-257 (294)
322 PRK15427 colanic acid biosynth 20.0 91 0.002 30.7 2.9 44 172-215 265-308 (406)
No 1
>KOG2648 consensus Diphthamide biosynthesis protein [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=4.8e-81 Score=608.73 Aligned_cols=286 Identities=48% Similarity=0.819 Sum_probs=252.1
Q ss_pred CCCCCCCCCcCE-EEEcccccCChHHHHHHHHHhCCCCC-eEEEEeccccHhHHHHHHHHHHhCC--CeEEecCCCCCCC
Q 042576 1 CLVPVDFTRIPC-LYVFVEIKIDVNRLIDTIKVNYSDPG-KLILAGTIQFASAIRAAKPELEKQG--FKVMIPQSKPLSA 76 (313)
Q Consensus 1 CL~Pv~~t~ipv-lYVFv~i~iD~~~~i~~i~~~f~~~~-~i~Lv~tiQf~~~l~~~~~~L~~~g--~~v~ipq~~pls~ 76 (313)
||+|++ ++|+ +||||+++||++|++++|+.+|++.. +|+|++|+||+|+++++++.|+..+ +++++||.+|+++
T Consensus 113 CLsp~~--~~~~~lYVf~~i~Idl~~~~~~l~~~~~~~~~~I~l~~~i~f~~~l~~~~~~L~~~~~~~~~i~Pq~~p~s~ 190 (453)
T KOG2648|consen 113 CLSPID--RLPVVLYVFVDIPIDLDHLVKSLQRNFPQLISQIVLLGTIQFAHSLEALATELKEELLDLEVILPQFKPLSP 190 (453)
T ss_pred ccCccc--cCCceEEEeecccccHHHHHHHHHhhcccccceeEEeechhhhHHHHHHHHHHhhccCceEEeccCCCCCCC
Confidence 999985 5555 99999999999999999999999766 7999999999999999999998775 7899999999999
Q ss_pred ccccCCCCCCCCCCCCCCeEEEecCCcccHHHHHhhCCCceEEEeCCCCCcccccccChHHHHHHHHHHHHHHhhcCCEE
Q 042576 77 GEVLGCTAPKIPARESDFNLVFIADGRFHLEAFMISNPGIKTFRYDPYLGKLFLEEYDNKGMRETRKRAIEKAMKEARTW 156 (313)
Q Consensus 77 GevLGCt~~~~~~~~~~d~iv~igdGrFHle~~mi~np~~~~y~yDPys~~~~~e~~d~~~~l~~R~~~I~kak~~A~~~ 156 (313)
||++|||+|..++....+++||+|||+||+++.||+||..++|+||||+++++.|.|++.+|+++||++|+||| +|++|
T Consensus 191 ~e~lG~t~p~~~~~~~~~~li~iGD~~~~le~~mi~np~~~~~~ydp~s~kl~~E~y~~~~m~~rR~~~vekar-dA~~i 269 (453)
T KOG2648|consen 191 GEVLGCTSPLLEGREEYDALIFIGDGRFHLESSMIANPGLPAYRYDPYSKKLTRESYDHSRMLRRRYYLVEKAR-DARTI 269 (453)
T ss_pred ccccceeccCCCCccccceEEEecCCCcchhHHHHhCCCCCeEEeCCccCceeecccchHHHHHHHHHHHHHHh-cCCeE
Confidence 99999999998763457899999999999999999999999999999999999999999999999999999999 99999
Q ss_pred EEEEeCCCCCCcHHHHHHHHHHHHHcCCcEEEEEeCCCCHHHHhcCcCCccEEEEecCCCccccccCCCCCcccCHHHHH
Q 042576 157 GIVLGTLGRQGNPRILERLQKRMEKKGFDYVVIMMSEISPARVALFEDSVDAWIQIACPRLSIDWGDAFTKPLLTPFEAE 236 (313)
Q Consensus 157 GIIvgTLg~Q~~~~ii~~l~~ll~~~Gkk~y~i~v~einp~KLanf~~~ID~fV~iaCPrlsid~~~~f~kPvLTPyE~~ 236 (313)
|||+||||+||+++++++|+++|+++|||+|+|+||||||+|||||+ |||+||||||||+|||||++|+||||||||++
T Consensus 270 GlivGTLG~qg~~~vl~~L~~~~~~~Gkk~y~l~~g~inPaKLAnF~-eIDvfV~iaCp~lsid~s~~F~kPiltPfEa~ 348 (453)
T KOG2648|consen 270 GLIVGTLGRQGNREVLEHLRKLLKAAGKKSYVLALGEINPAKLANFP-EIDVFVQIACPRLSIDWSKEFYKPLLTPFEAE 348 (453)
T ss_pred EEEEecccccCCHHHHHHHHHHHHHcCCceEEEEecCCCHHHhcCCc-cccEEEEEeCcccchhhhhhhccccccHHHHH
Confidence 99999999999999999999999999999999999999999999999 89999999999999999999999999999999
Q ss_pred HHhCCCCcccccchhhhhhhhhcccCCCCCCCCCCCCCCCCCCcceeccCC-C-C--Cccccc
Q 042576 237 IALGVIPGWWERDKEREREREESKSCGGCGNEDKNCDGDGDYPMDYYAQDG-G-E--WNSSYV 295 (313)
Q Consensus 237 vAL~~~~~~w~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ypmd~y~~~~-g-~--w~~~~~ 295 (313)
+||+.. .||.+..... -+....|.......- ...+.||||||+..| | + ||++..
T Consensus 349 ~Al~~~-~W~~~~~~~~--~~~~~~~~~~~~~~~--~~~~d~pm~~~~~~~~~~~~~~~~~~~ 406 (453)
T KOG2648|consen 349 VALNPI-AWTGDYLAPF--VTAIKLLLKESEFHS--SELGDYPMDYYSLGSLGPPPAWTSSND 406 (453)
T ss_pred HhcCcc-ccCCccccch--hhHHhhhhccccccc--cccccCcccccccccCCcCcccCCccc
Confidence 999987 8887531110 011111111111111 123579999999987 4 5 998743
No 2
>TIGR00322 diphth2_R diphthamide biosynthesis protein 2-related domain. Because archaeal species are known to have the diphthamide modification to the conserved His of archaeal and eukaryotic EF-2, it may be that the lone homolog of YKL191W in M. jannaschii, A. fulgidus, and M. thermoautotrophicum is orthologous. However, each of these is considerably shorter than YKL191W and seems more closely related to the uncharacterized protein YIL103W than to YKL191W.
Probab=100.00 E-value=1.8e-74 Score=555.52 Aligned_cols=240 Identities=38% Similarity=0.665 Sum_probs=226.5
Q ss_pred CCCCCCCCCcCEEEEcccccCChHHHHHHHHHhCCCCCeEEEEeccccHhHHHHHHHHHHhCCCeEEe--cCCCCCCCcc
Q 042576 1 CLVPVDFTRIPCLYVFVEIKIDVNRLIDTIKVNYSDPGKLILAGTIQFASAIRAAKPELEKQGFKVMI--PQSKPLSAGE 78 (313)
Q Consensus 1 CL~Pv~~t~ipvlYVFv~i~iD~~~~i~~i~~~f~~~~~i~Lv~tiQf~~~l~~~~~~L~~~g~~v~i--pq~~pls~Ge 78 (313)
||+|+.. ++||+|||+++++|++++++++++++++.++|+|++|+||.|.++++++.|++.|+++++ ||.+|++|||
T Consensus 82 cl~~~~~-~~pv~yVf~~~~~d~~~~~~~~~~~~~~~~~i~l~~tiq~~~~~~~~~~~L~~~g~~v~i~~~~~~~~~~g~ 160 (332)
T TIGR00322 82 PLVPDDV-EIKVLYVPVTINIEYDHIIKTLQDNFPKGRRIATIGTAQFNHKLHSVRDKLLNEGHEVYIGPPQGKPLSRGQ 160 (332)
T ss_pred CCCcccC-CCCEEEEEccCCCCHHHHHHHHHHHcCCCCeEEEEECHHHHHHHHHHHHHHHhcCceEEEecCccCCCCCcc
Confidence 9999632 889999999999999999999999998767899999999999999999999999999665 6789999999
Q ss_pred ccCCCCCCCCCCCCCCeEEEecCCcccHHHHHhhCCCceEEEeCCCCCcccccccChHHHHHHHHHHHHHHhhcCCEEEE
Q 042576 79 VLGCTAPKIPARESDFNLVFIADGRFHLEAFMISNPGIKTFRYDPYLGKLFLEEYDNKGMRETRKRAIEKAMKEARTWGI 158 (313)
Q Consensus 79 vLGCt~~~~~~~~~~d~iv~igdGrFHle~~mi~np~~~~y~yDPys~~~~~e~~d~~~~l~~R~~~I~kak~~A~~~GI 158 (313)
||||+++.+.+ .+.|+++|||+|+||++++||++ .+++|+|||++++++++++++++++++|+++|+||+ +|++|||
T Consensus 161 vLGC~~~~~~~-~~~d~~l~vg~g~FH~~~~~l~~-~~~v~~~DP~s~~~~~~~~~~~~~l~rR~~~I~ka~-~A~~vGI 237 (332)
T TIGR00322 161 VLGCNSEVLRG-EQADAMVFIGDGRFHPLGAAIHT-EKEVFKYDPYSGEFTRIGEDAKQFVKVRALAISKAR-KGKKFGV 237 (332)
T ss_pred ccCCCcCCCCC-CCCCEEEEEcCCcchHHHHHHHc-CCcEEEECCCCCceeEccccHHHHHHHHHHHHHHHh-cCCEEEE
Confidence 99999998853 24689999999999999999986 899999999999999999999999999999999999 9999999
Q ss_pred EEeCCCCCCcHHHHHHHHHHHHHcCCcEEEEEeCCCCHHHHhcCcCCccEEEEecCCCccccccCCCCCcccCHHHHHHH
Q 042576 159 VLGTLGRQGNPRILERLQKRMEKKGFDYVVIMMSEISPARVALFEDSVDAWIQIACPRLSIDWGDAFTKPLLTPFEAEIA 238 (313)
Q Consensus 159 IvgTLg~Q~~~~ii~~l~~ll~~~Gkk~y~i~v~einp~KLanf~~~ID~fV~iaCPrlsid~~~~f~kPvLTPyE~~vA 238 (313)
|+||||+||+++++++|+++|+++|||+|+|++|+|||+||+||+ +||+|||+||||+||||+.+|+||||||||++||
T Consensus 238 lvgTl~~q~~~~~~~~l~~ll~~~gkk~y~i~~~~in~~kL~nf~-eiD~fV~~aCPr~sidd~~~f~kPvlTP~E~e~a 316 (332)
T TIGR00322 238 VLSSKGGQGRLRLAKNLKKNLEEAGKTVLIILLSNVSPAKLLMFD-QIDVFVQVACPRIAIDDGYLFNKPLLTPYEFELL 316 (332)
T ss_pred EEecCccCCCHHHHHHHHHHHHHcCCcEEEEEeCCCCHHHHhCCC-CcCEEEEecCCCceecchhhcCCccccHHHHHHH
Confidence 999999999999999999999999999999999999999999999 8999999999999999999999999999999999
Q ss_pred hCCCCcccc
Q 042576 239 LGVIPGWWE 247 (313)
Q Consensus 239 L~~~~~~w~ 247 (313)
||.. .|+
T Consensus 317 l~~~--~~~ 323 (332)
T TIGR00322 317 LKKR--VEK 323 (332)
T ss_pred hCcc--ccc
Confidence 9874 365
No 3
>TIGR03682 arCOG04112 arCOG04112 universal archaeal diphthamide biosynthesis domain protein. This family of proteins has been observed universally in archaeal genomes and contains a match to the TIGR00322 model for the diphthamide biosynthesis protein 2-related domain.
Probab=100.00 E-value=1.6e-70 Score=523.48 Aligned_cols=234 Identities=29% Similarity=0.472 Sum_probs=221.7
Q ss_pred CCCCCCCCCcCEEEEcccccCChHHHHHHHHHhCCCCCeEEEEeccccHhHHHHHHHHHHhCCCeEEecCCC--CCCCcc
Q 042576 1 CLVPVDFTRIPCLYVFVEIKIDVNRLIDTIKVNYSDPGKLILAGTIQFASAIRAAKPELEKQGFKVMIPQSK--PLSAGE 78 (313)
Q Consensus 1 CL~Pv~~t~ipvlYVFv~i~iD~~~~i~~i~~~f~~~~~i~Lv~tiQf~~~l~~~~~~L~~~g~~v~ipq~~--pls~Ge 78 (313)
||++. ++++||+|||++.++|++++++++.++++ .++|+|++|+||.|.++++++.|+++|+++++++.+ |+++||
T Consensus 63 cl~~~-~~~~pv~yV~~~~~~d~~~~~~~~~~~~~-~~~v~l~~tiq~~~~~~~v~~~L~~~g~~v~i~~~~~~~~~~g~ 140 (308)
T TIGR03682 63 PLPNV-KPEIPVIFIEARSDVDVEEVIEKALEELK-GRRIGLVTTAQHVHLLEKVKEILEERGIEVVIGKGDGRVTYPGQ 140 (308)
T ss_pred CCCcc-cCCCCEEEEEecCCcCHHHHHHHHHHHCC-CCeEEEEEcHHhHHHHHHHHHHHHHcCceEEecCCCCCCCCCce
Confidence 78632 46899999999999999999999999997 468999999999999999999999999999999864 999999
Q ss_pred ccCCCCCCCCCCCCCCeEEEecCCcccHHHHHhhCCCceEEEeCCCCCcccccccChHHHHHHHHHHHHHHhhcCCEEEE
Q 042576 79 VLGCTAPKIPARESDFNLVFIADGRFHLEAFMISNPGIKTFRYDPYLGKLFLEEYDNKGMRETRKRAIEKAMKEARTWGI 158 (313)
Q Consensus 79 vLGCt~~~~~~~~~~d~iv~igdGrFHle~~mi~np~~~~y~yDPys~~~~~e~~d~~~~l~~R~~~I~kak~~A~~~GI 158 (313)
||||+++...+. +.|+++|||+|+||++++|| +|.+++|+|||++++++.+++++++++++|+++|+||+ +|++|||
T Consensus 141 vlGC~~~~~~~~-~~d~~~~vg~g~Fh~~~l~l-~~~~~v~~~DP~~~~~~~~~~~~~~~l~~R~~~I~ka~-~A~~vGI 217 (308)
T TIGR03682 141 VLGCNFSAARSV-DADAFLFVGTGLFHPLGLAL-ATNKPVYAADPFSGEVEDIEAEIDKFLRVRYARISKAL-DAKKFGI 217 (308)
T ss_pred eeCccccCCCCC-CccEEEEEcCCcchHHHHHh-ccCCcEEEECCCCCceEeechhHHHHHHHHHHHHHHHh-hCCeEEE
Confidence 999999988642 46899999999999999999 79999999999999999999999999999999999999 9999999
Q ss_pred EEeCCCCCCcHHHHHHHHHHHHHcCCcEEEEEeCCCCHHHHhcCcCCccEEEEecCCCccccccCCCCCcccCHHHHHHH
Q 042576 159 VLGTLGRQGNPRILERLQKRMEKKGFDYVVIMMSEISPARVALFEDSVDAWIQIACPRLSIDWGDAFTKPLLTPFEAEIA 238 (313)
Q Consensus 159 IvgTLg~Q~~~~ii~~l~~ll~~~Gkk~y~i~v~einp~KLanf~~~ID~fV~iaCPrlsid~~~~f~kPvLTPyE~~vA 238 (313)
|+||||+||+++++++|+++|+++|||+|+|+||+|||+||+||+ ||+||++||||+||||+.+|+||||||||+++|
T Consensus 218 lvgTl~~q~~~~~~~~l~~ll~~~gkk~y~i~~~~in~~kL~nf~--iD~fV~~aCPr~sidd~~~f~kPvlTP~E~~~a 295 (308)
T TIGR03682 218 LVSTKKGQRRPELAEELKKLLEELGKEALLILLDNISPDQLRNLD--FDAYVNTACPRIAIDDYARFKKPVLTPQEFEIV 295 (308)
T ss_pred EEEccCcCCCHHHHHHHHHHHHHcCCeEEEEEeCCCCHHHHhcCC--cCEEEEccCCCcccccHhhCCCcccCHHHHHHH
Confidence 999999999999999999999999999999999999999999995 999999999999999999999999999999999
Q ss_pred hCC
Q 042576 239 LGV 241 (313)
Q Consensus 239 L~~ 241 (313)
||.
T Consensus 296 l~~ 298 (308)
T TIGR03682 296 LGK 298 (308)
T ss_pred hCC
Confidence 986
No 4
>PF01866 Diphthamide_syn: Putative diphthamide synthesis protein; InterPro: IPR002728 Members of this family include Q16439 from SWISSPROT, a candidate tumour suppressor gene [], and DPH2 from yeast P32461 from SWISSPROT [], which confers resistance to diphtheria toxin and has been found to be involved in diphthamide synthesis. Diphtheria toxin inhibits eukaryotic protein synthesis by ADP-ribosylating diphthamide, a posttranslationally modified histidine residue present in EF2. The exact function of the members of this family is unknown.; GO: 0017183 peptidyl-diphthamide biosynthetic process from peptidyl-histidine, 0005737 cytoplasm; PDB: 3LZD_B 3LZC_A.
Probab=100.00 E-value=6.4e-71 Score=525.71 Aligned_cols=241 Identities=46% Similarity=0.819 Sum_probs=179.1
Q ss_pred CCCCCCCCCcCEEEEcccccCChHHHHHHHHHhCCCCCeEEEEeccccHhHHHHHHHHHHhCCCeEE--ecCCCCCCCcc
Q 042576 1 CLVPVDFTRIPCLYVFVEIKIDVNRLIDTIKVNYSDPGKLILAGTIQFASAIRAAKPELEKQGFKVM--IPQSKPLSAGE 78 (313)
Q Consensus 1 CL~Pv~~t~ipvlYVFv~i~iD~~~~i~~i~~~f~~~~~i~Lv~tiQf~~~l~~~~~~L~~~g~~v~--ipq~~pls~Ge 78 (313)
||+|+ ++++||+|||+++++|++++++.+.+.+++.++|+|++|+||.|.++++++.|+++|+... .|+.+|+++||
T Consensus 56 cl~~~-~~~ipviyV~~~~~id~~~~~~~~~~~~~~~~~i~l~~~vqy~~~~~~~~~~L~~~g~~~~i~~~~~~~~~~g~ 134 (307)
T PF01866_consen 56 CLSPT-KPRIPVIYVFVEINIDVEHLVESLKEEFKKKKKIVLLTDVQYAHALEELKEILREKGFEVVIGIPQNRPLSPGQ 134 (307)
T ss_dssp --S-----SS-EEEEE--B-S-HHHHHHHTHHHHHT-SEEEEEE-GGGGGGHHHHHHHHHHTT-EEE-----TT-SSTTB
T ss_pred CCCcc-cccCceEEEeccCCCCHHHHHHHHHHhccCCceEEEEEehhHHHHHHHHHHHHHHhcccccccCCccccCCccc
Confidence 89995 3589999999999999999999999999776889999999999999999999999988754 47889999999
Q ss_pred ccCCCCCCCCCCCCCCeEEEecCCcccHHHHHhhCCCceEEEeCCCCCccccc--ccChHHHHHHHHHHHHHHhhcCCEE
Q 042576 79 VLGCTAPKIPARESDFNLVFIADGRFHLEAFMISNPGIKTFRYDPYLGKLFLE--EYDNKGMRETRKRAIEKAMKEARTW 156 (313)
Q Consensus 79 vLGCt~~~~~~~~~~d~iv~igdGrFHle~~mi~np~~~~y~yDPys~~~~~e--~~d~~~~l~~R~~~I~kak~~A~~~ 156 (313)
||||+++.++...+.++++|||+|+||++++||+ |.+++|+|||++++++.| .++.++++++|+++|+||+ +|++|
T Consensus 135 vlGc~~~~~~~~~~~~~~l~IG~g~fh~~~l~l~-~~~~v~~~dP~~~~~~~e~~~~~~~~~l~~R~~~i~ka~-~a~~~ 212 (307)
T PF01866_consen 135 VLGCTYPSADSLDDDDAILFIGGGRFHLLGLMLS-PGKPVYRYDPYSKTLSVEDISYDIERLLRRRYALIEKAK-DAKTF 212 (307)
T ss_dssp -BTTB-GGG-S--S-SEEEEESSSSHHHHHHHHH-H-SEEEEE-TT--T--EEE----THHHHHHHHHHHHHHT-T--EE
T ss_pred ccCCccCcccccccccEEEEEcCCchHHHHHHHh-cCCCEEEeCCCcccceeecccccHHHHHHHHHHHHHHHh-cCCEE
Confidence 9999999886412369999999999999999999 999999999998888888 7799999999999999999 99999
Q ss_pred EEEEeCCCCCCcHHHHHHHHHHHHHcCCcEEEEEeCCCCHHHHhcCcCCccEEEEecCCCccccccCCCCCcccCHHHHH
Q 042576 157 GIVLGTLGRQGNPRILERLQKRMEKKGFDYVVIMMSEISPARVALFEDSVDAWIQIACPRLSIDWGDAFTKPLLTPFEAE 236 (313)
Q Consensus 157 GIIvgTLg~Q~~~~ii~~l~~ll~~~Gkk~y~i~v~einp~KLanf~~~ID~fV~iaCPrlsid~~~~f~kPvLTPyE~~ 236 (313)
|||+||||+|+|++++++|+++|+++|||+|+|+|++|||+||+||+ +||+||++||||+||||+++|+||||||||++
T Consensus 213 GIiv~tl~~q~~~~~~~~l~~~l~~~gkk~y~~~~~~i~~~kL~nf~-eid~fV~~aCPr~~idd~~~f~kPvltP~E~~ 291 (307)
T PF01866_consen 213 GIIVGTLGGQGYLELIKRLKKLLKKAGKKSYTLSVGEINPAKLANFP-EIDAFVQIACPRLSIDDSKDFYKPVLTPYELE 291 (307)
T ss_dssp EEEEE-STTT--HHHHHHHHHHHHHTT-EEEEEEESS--GGGGTTS----SEEEE-S-THHHHT--S--SS-EE-HHHHH
T ss_pred EEEEecCCCCCCHHHHHHHHHHHHHcCCEEEEEEECCCCHHHHhcCc-ccCEEEEecCCCcccCchhhcCCcccCHHHHH
Confidence 99999999999999999999999999999999999999999999999 89999999999999999999999999999999
Q ss_pred HHhCCCCcccc
Q 042576 237 IALGVIPGWWE 247 (313)
Q Consensus 237 vAL~~~~~~w~ 247 (313)
|||+. .||+
T Consensus 292 ~al~~--~~~~ 300 (307)
T PF01866_consen 292 VALNE--REWG 300 (307)
T ss_dssp HHTTS---S--
T ss_pred HHhCC--cccC
Confidence 99987 4465
No 5
>TIGR00272 DPH2 diphthamide biosynthesis protein 2. This protein has been shown in Saccharomyces cerevisiae to be one of several required for the modification of a particular histidine residue of translation elongation factor 2 to diphthamide. This modified site can then become the target for ADP-ribosylation by diphtheria toxin.
Probab=100.00 E-value=1.4e-62 Score=493.46 Aligned_cols=245 Identities=22% Similarity=0.389 Sum_probs=219.1
Q ss_pred CCCCCCCCCcCEEEEcccccCChHHHHHHHHHhCCC-CCeEEEEeccccHhHHHHHHHHHHhC------CCeEEecCCCC
Q 042576 1 CLVPVDFTRIPCLYVFVEIKIDVNRLIDTIKVNYSD-PGKLILAGTIQFASAIRAAKPELEKQ------GFKVMIPQSKP 73 (313)
Q Consensus 1 CL~Pv~~t~ipvlYVFv~i~iD~~~~i~~i~~~f~~-~~~i~Lv~tiQf~~~l~~~~~~L~~~------g~~v~ipq~~p 73 (313)
||+|+ +++||+|||+++++|++++++++++++++ .++|+|++|+||.|+++++++.|++. ..++..||.+|
T Consensus 117 CLsp~--~~lPviYVf~~~~~d~~~~~~~~~~~~~~~~~kV~l~~dvqy~~~~~~l~~~L~~~~~~~~~~~~~~~~~~~~ 194 (496)
T TIGR00272 117 CLSAI--QNLPVVYVFGTPPIDLALVVENFQRAFPDLSSKICLMADAPFSKHQSQLYNILKEVLPGDLHYTNIIYPQVNT 194 (496)
T ss_pred CCCCC--CCCCEEEEeccCCCCHHHHHHHHHHhccccCCeEEEEEchhHHHHHHHHHHHHHhhccccccccceecccccc
Confidence 99996 58999999999999999999999999886 55799999999999999999999852 24578899998
Q ss_pred CCCcc---ccCCCCCCCCCCC-CCCeEEEecCCcc-cHHHHHhh-CCC-ceEEEeCCCCCcccccccC-hHHHHHHHHHH
Q 042576 74 LSAGE---VLGCTAPKIPARE-SDFNLVFIADGRF-HLEAFMIS-NPG-IKTFRYDPYLGKLFLEEYD-NKGMRETRKRA 145 (313)
Q Consensus 74 ls~Ge---vLGCt~~~~~~~~-~~d~iv~igdGrF-Hle~~mi~-np~-~~~y~yDPys~~~~~e~~d-~~~~l~~R~~~ 145 (313)
++.|+ ||||+++.+.+.. +...++|||+|+| |+.+++|+ +|. +++|+|||++++++.+.++ +.++||+||++
T Consensus 195 ~~~~~~~~vlGc~~~~~~~~~~~~~~~l~IG~~~~g~f~~l~l~~~~~~~~v~~~dP~~~~~~~~~~~~~~~~L~rRy~~ 274 (496)
T TIGR00272 195 SAVEEKFVTIGRTFHVPEDVDQQEKNLVLFGQHSSEDLHLIHLTTYQDLSTVFQFVPIFDPILPESVTGPFPSLRRRYKL 274 (496)
T ss_pred ccCCCCceecCccccCccccccccceEEEEcCCCchhhhHhhhhcCCCCCceEEECCCCCcceecccchHHHHHHHHHHH
Confidence 88765 9999998774221 1235899999777 66667654 545 5699999999999999877 99999999999
Q ss_pred HHHHhhcCCEEEEEEeCCCCCCcHHHHHHHHHHHHHcCCcEEEEEeCCCCHHHHhcCcCCccEEEEecCCCccccccCCC
Q 042576 146 IEKAMKEARTWGIVLGTLGRQGNPRILERLQKRMEKKGFDYVVIMMSEISPARVALFEDSVDAWIQIACPRLSIDWGDAF 225 (313)
Q Consensus 146 I~kak~~A~~~GIIvgTLg~Q~~~~ii~~l~~ll~~~Gkk~y~i~v~einp~KLanf~~~ID~fV~iaCPrlsid~~~~f 225 (313)
|+||| +|++|||||||||+|+|++++++|+++|+++|||+|+|+||+|||+||+||+ +||+||+|||||+||||+++|
T Consensus 275 I~kA~-~A~~~GIlVgTL~~q~~~~ii~~l~~li~~~GkK~yl~~vgkinpaKLaNF~-eID~fV~vaCPr~sidd~~~F 352 (496)
T TIGR00272 275 VHVAR-DAGCIGIVVGTLGVRNTRETINELRKMIKTAGKKHYLFVVGKPNPAKLANFE-DIDIFVLLGCSQSGIIDSNEF 352 (496)
T ss_pred HHHHh-cCCEEEEEEecCccCCCHHHHHHHHHHHHHcCCcEEEEEeCCCCHHHHhCCC-CCCEEEEccCCCcccccHhhC
Confidence 99999 9999999999999999999999999999999999999999999999999998 899999999999999999999
Q ss_pred CCcccCHHHHHHHhCCCCcccccc
Q 042576 226 TKPLLTPFEAEIALGVIPGWWERD 249 (313)
Q Consensus 226 ~kPvLTPyE~~vAL~~~~~~w~~~ 249 (313)
+||||||||++|||+....|+.+.
T Consensus 353 ~KPVlTP~ElelAL~~~~~w~~~~ 376 (496)
T TIGR00272 353 YRPIVTPFELNLALSEEVTWVVDF 376 (496)
T ss_pred CCceecHHHHHHHhCCcccccchH
Confidence 999999999999999876676553
No 6
>COG1736 DPH2 Diphthamide synthase subunit DPH2 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=1.8e-62 Score=471.22 Aligned_cols=256 Identities=34% Similarity=0.564 Sum_probs=238.5
Q ss_pred CCCCCCCCCcCEEEEcccccCChHHHHHHHHHhCCCC-CeEEEEeccccHhHHHHHHHHHHhCCCeEEe--cCCCCCCCc
Q 042576 1 CLVPVDFTRIPCLYVFVEIKIDVNRLIDTIKVNYSDP-GKLILAGTIQFASAIRAAKPELEKQGFKVMI--PQSKPLSAG 77 (313)
Q Consensus 1 CL~Pv~~t~ipvlYVFv~i~iD~~~~i~~i~~~f~~~-~~i~Lv~tiQf~~~l~~~~~~L~~~g~~v~i--pq~~pls~G 77 (313)
||.|. ...+||+|||...++|+++.++....+++.. +||+|++|+||.+.++.+++.|+..|+.+++ ||.+++++|
T Consensus 86 ~l~~~-~~~~~Viyv~~~~~~d~~~~~~~~~~~l~~~~r~I~li~t~q~~~~l~~~k~~L~~~g~~v~i~~~~~r~~~~g 164 (347)
T COG1736 86 CLPPV-EYELPVIYVFAFSRVDVDLVVLEATRELKKGSRRIGLITTAQHVHLLEEVKEILEGRGYEVVIGRGQTRPAYPG 164 (347)
T ss_pred cCCCc-CCCCcEEEeecccccchhHHHHHhhHhhccCCceEEEEecccchhHHHHHHHHhhcCCeEEEEeCCCCcccCcc
Confidence 67774 5689999999999999999999998888864 4699999999999999999999999998776 677899999
Q ss_pred cccCCCCCCCCCCCCCCeEEEecCCcccHHHHHhhCCCceEEEeCCCCCcccccccChHHHHHHHHHHHHHHhhcCCEEE
Q 042576 78 EVLGCTAPKIPARESDFNLVFIADGRFHLEAFMISNPGIKTFRYDPYLGKLFLEEYDNKGMRETRKRAIEKAMKEARTWG 157 (313)
Q Consensus 78 evLGCt~~~~~~~~~~d~iv~igdGrFHle~~mi~np~~~~y~yDPys~~~~~e~~d~~~~l~~R~~~I~kak~~A~~~G 157 (313)
||||||++.+++ .+.|+++|||+|+||+++++|. |.+++|+||||+++++.++.++++++++|+++|.+|+ +|++||
T Consensus 165 qVLGC~~~~~~~-~~~d~~l~vg~G~FH~lg~~i~-~~~~v~~~dP~s~~~~~~~~~~~~~l~~R~~~i~~a~-~a~~~g 241 (347)
T COG1736 165 QVLGCNFSVLEG-VDADAVLYVGSGRFHPLGLAIR-TEKPVFAIDPYSGKVREEDPEADRFLRKRYAAISKAL-DAKSFG 241 (347)
T ss_pred eeeccccccCCc-cccceEEEEcCCccChhhcccc-cCCcEEEEcCCCCceeecchhhhHHHHHHHHHHHHHh-cCCeEE
Confidence 999999999975 3479999999999999999999 9999999999999999999999999999999999999 999999
Q ss_pred EEEeCCCCCCcHHHHHHHHHHHHHcCCcEEEEEeCCCCHHHHhcCcCCccEEEEecCCCccccccCCCCCcccCHHHHHH
Q 042576 158 IVLGTLGRQGNPRILERLQKRMEKKGFDYVVIMMSEISPARVALFEDSVDAWIQIACPRLSIDWGDAFTKPLLTPFEAEI 237 (313)
Q Consensus 158 IIvgTLg~Q~~~~ii~~l~~ll~~~Gkk~y~i~v~einp~KLanf~~~ID~fV~iaCPrlsid~~~~f~kPvLTPyE~~v 237 (313)
||+||+++|+++++++.|.++++++||++|+|+++++||+||+||. +||+||++||||++|||+..|.||||||||+++
T Consensus 242 iiv~tk~gQ~r~~~~~~l~k~~~~~g~~~~li~~~~i~p~~L~~f~-~iD~~v~taCPRi~iDd~~~f~kPlLTP~E~~~ 320 (347)
T COG1736 242 IIVSTKGGQRRLEVARELVKLLKEAGKEVYLIVVDEISPDKLANFD-DIDAFVNTACPRIPIDDGDRFKKPLLTPYEFEI 320 (347)
T ss_pred EEEecccccCcHHHHHHHHHHHHHcCCceEEEEecCCCHHHHhccc-ceeEEEEecCCCcccchHhhhCCcccChHHHHH
Confidence 9999999999999999999999999999999999999999999998 799999999999999999999999999999999
Q ss_pred HhCCCCcccccchhhhhhhhhcccCCCCCCCCCCCCCCCCCCcceeccCC-CCCcc
Q 042576 238 ALGVIPGWWERDKEREREREESKSCGGCGNEDKNCDGDGDYPMDYYAQDG-GEWNS 292 (313)
Q Consensus 238 AL~~~~~~w~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ypmd~y~~~~-g~w~~ 292 (313)
||+ ..||+ .|+||++..++ |+|+.
T Consensus 321 ~l~--~~~~~-----------------------------~y~~Dei~~~~~~~~~~ 345 (347)
T COG1736 321 ALG--WRSDE-----------------------------RYAFDEIVGNDGGPDEY 345 (347)
T ss_pred hhc--cCccc-----------------------------ccccceeecCCCCCCCc
Confidence 998 24555 59999999775 77763
No 7
>COG1609 PurR Transcriptional regulators [Transcription]
Probab=90.02 E-value=8.3 Score=37.23 Aligned_cols=151 Identities=13% Similarity=0.139 Sum_probs=86.7
Q ss_pred eEEEEec----cccHhHHHHHHHHHHhCCCeEEecCCCCCCCccccCCCCCCCCCCCCCCeEEEecCCcccHHHHHhhCC
Q 042576 39 KLILAGT----IQFASAIRAAKPELEKQGFKVMIPQSKPLSAGEVLGCTAPKIPARESDFNLVFIADGRFHLEAFMISNP 114 (313)
Q Consensus 39 ~i~Lv~t----iQf~~~l~~~~~~L~~~g~~v~ipq~~pls~GevLGCt~~~~~~~~~~d~iv~igdGrFHle~~mi~np 114 (313)
.|+++.. ..|...++.+.+.++++|+.+++..... ++.+.--+...... ..+|.+|+.+...-+..--++...
T Consensus 60 ~Ig~i~p~~~~~~~~~i~~gi~~~~~~~gy~~~l~~~~~-~~~~e~~~~~~l~~--~~vdGiIi~~~~~~~~~~~~l~~~ 136 (333)
T COG1609 60 TIGLVVPDITNPFFAEILKGIEEAAREAGYSLLLANTDD-DPEKEREYLETLLQ--KRVDGLILLGERPNDSLLELLAAA 136 (333)
T ss_pred EEEEEeCCCCCchHHHHHHHHHHHHHHcCCEEEEECCCC-CHHHHHHHHHHHHH--cCCCEEEEecCCCCHHHHHHHHhc
Confidence 4776643 6788889999999999999987632211 00000000000001 248999999832222333344445
Q ss_pred CceEEEeCCCCC--cccccccChHHHHHHHHHHHHHHh-hcCCEEEEEEeCCCCCCcHHHHHHHHHHHHHcCCcE--EEE
Q 042576 115 GIKTFRYDPYLG--KLFLEEYDNKGMRETRKRAIEKAM-KEARTWGIVLGTLGRQGNPRILERLQKRMEKKGFDY--VVI 189 (313)
Q Consensus 115 ~~~~y~yDPys~--~~~~e~~d~~~~l~~R~~~I~kak-~~A~~~GIIvgTLg~Q~~~~ii~~l~~ll~~~Gkk~--y~i 189 (313)
..|++.+|-... .+.....|.... -| .+++... ..-+++|+|-|.........-.+-.++-++++|.+. ..+
T Consensus 137 ~~P~V~i~~~~~~~~~~~V~~Dn~~~--~~-~a~~~L~~~G~~~i~~i~~~~~~~~~~~R~~Gf~~al~~~~~~~~~~~i 213 (333)
T COG1609 137 GIPVVVIDRSPPGLGVPSVGIDNFAG--AY-LATEHLIELGHRRIAFIGGPLDSSASRERLEGYRAALREAGLPINPEWI 213 (333)
T ss_pred CCCEEEEeCCCccCCCCEEEEChHHH--HH-HHHHHHHHCCCceEEEEeCCCccccHhHHHHHHHHHHHHCCCCCCcceE
Confidence 788888885433 333333443322 22 2333333 035899999999855555666777788889999873 555
Q ss_pred EeCCCC
Q 042576 190 MMSEIS 195 (313)
Q Consensus 190 ~v~ein 195 (313)
.-++.+
T Consensus 214 ~~~~~~ 219 (333)
T COG1609 214 VEGDFS 219 (333)
T ss_pred EecCCC
Confidence 554444
No 8
>PF00532 Peripla_BP_1: Periplasmic binding proteins and sugar binding domain of LacI family; InterPro: IPR001761 This family includes the periplasmic binding proteins, and the LacI family transcriptional regulators. The periplasmic binding proteins are the primary receptors for chemotaxis and transport of many sugar based solutes. The LacI family of proteins consist of transcriptional regulators related to the lac repressor. In this case, generally the sugar binding domain binds a sugar which changes the DNA binding activity of the repressor domain (lacI) [, ].; PDB: 1BAP_A 7ABP_A 6ABP_A 1ABF_A 5ABP_A 2WRZ_B 9ABP_A 1APB_A 1ABE_A 8ABP_A ....
Probab=85.72 E-value=29 Score=32.34 Aligned_cols=155 Identities=15% Similarity=0.183 Sum_probs=81.7
Q ss_pred cHhHHHHHHHHHHhCCCeEEecCCCCCCCc-cccCCCCCCCCCCCCCCeEEEecCCcccHHHHHhhCCCceEEEeCCCCC
Q 042576 48 FASAIRAAKPELEKQGFKVMIPQSKPLSAG-EVLGCTAPKIPARESDFNLVFIADGRFHLEAFMISNPGIKTFRYDPYLG 126 (313)
Q Consensus 48 f~~~l~~~~~~L~~~g~~v~ipq~~pls~G-evLGCt~~~~~~~~~~d~iv~igdGrFHle~~mi~np~~~~y~yDPys~ 126 (313)
|...+..+.+.++++||.+++-....-..- +.+- .+.. ..+|++|+.+...-...-..+...+.|++..|-+..
T Consensus 16 f~~ii~gIe~~a~~~Gy~l~l~~t~~~~~~e~~i~----~l~~-~~vDGiI~~s~~~~~~~l~~~~~~~iPvV~~~~~~~ 90 (279)
T PF00532_consen 16 FAEIIRGIEQEAREHGYQLLLCNTGDDEEKEEYIE----LLLQ-RRVDGIILASSENDDEELRRLIKSGIPVVLIDRYID 90 (279)
T ss_dssp HHHHHHHHHHHHHHTTCEEEEEEETTTHHHHHHHH----HHHH-TTSSEEEEESSSCTCHHHHHHHHTTSEEEEESS-SC
T ss_pred HHHHHHHHHHHHHHcCCEEEEecCCCchHHHHHHH----HHHh-cCCCEEEEecccCChHHHHHHHHcCCCEEEEEeccC
Confidence 777788899999999999765221100000 1110 0000 247999888543321221223333789999997733
Q ss_pred c---ccccccChHHH-HHHHHHHHHHHhhcCCE-EEEEEeCCCCCCcHHHHHHHHHHHHHcCC--cEEEEEeCCCCHH--
Q 042576 127 K---LFLEEYDNKGM-RETRKRAIEKAMKEART-WGIVLGTLGRQGNPRILERLQKRMEKKGF--DYVVIMMSEISPA-- 197 (313)
Q Consensus 127 ~---~~~e~~d~~~~-l~~R~~~I~kak~~A~~-~GIIvgTLg~Q~~~~ii~~l~~ll~~~Gk--k~y~i~v~einp~-- 197 (313)
. +.....|..+. ...=.++++ + .-++ |++|-|.........-++-.++-++++|. +-..+.-+.-+.+
T Consensus 91 ~~~~~~~V~~D~~~a~~~a~~~Li~--~-Gh~~~I~~i~~~~~~~~~~~R~~Gy~~Al~~~Gl~~~~~~i~~~~~~~~~g 167 (279)
T PF00532_consen 91 NPEGVPSVYIDNYEAGYEATEYLIK--K-GHRRPIAFIGGPEDSSTSRERLQGYRDALKEAGLPIDEEWIFEGDFDYESG 167 (279)
T ss_dssp TTCTSCEEEEEHHHHHHHHHHHHHH--T-TCCSTEEEEEESTTTHHHHHHHHHHHHHHHHTTSCEEEEEEEESSSSHHHH
T ss_pred CcccCCEEEEcchHHHHHHHHHHHh--c-ccCCeEEEEecCcchHHHHHHHHHHHHHHHHcCCCCCcccccccCCCHHHH
Confidence 2 22222332221 111122222 2 5578 99999987665444445556888999998 3444455555532
Q ss_pred ------HHhcCcCCccEEEE
Q 042576 198 ------RVALFEDSVDAWIQ 211 (313)
Q Consensus 198 ------KLanf~~~ID~fV~ 211 (313)
-|++-+ ++|+++-
T Consensus 168 ~~~~~~ll~~~p-~idai~~ 186 (279)
T PF00532_consen 168 YEAARELLESHP-DIDAIFC 186 (279)
T ss_dssp HHHHHHHHHTST-T-SEEEE
T ss_pred HHHHHHHHhhCC-CCEEEEE
Confidence 233445 7887653
No 9
>PRK09492 treR trehalose repressor; Provisional
Probab=82.55 E-value=5 Score=37.20 Aligned_cols=78 Identities=17% Similarity=0.369 Sum_probs=51.0
Q ss_pred cCCEEEEEEeCCCCCCcHHHHHHHHHHHHHcCCcEEEEEeCCCCHHHH----hcCc-CCccEEEEecCCCccccccCCCC
Q 042576 152 EARTWGIVLGTLGRQGNPRILERLQKRMEKKGFDYVVIMMSEISPARV----ALFE-DSVDAWIQIACPRLSIDWGDAFT 226 (313)
Q Consensus 152 ~A~~~GIIvgTLg~Q~~~~ii~~l~~ll~~~Gkk~y~i~v~einp~KL----anf~-~~ID~fV~iaCPrlsid~~~~f~ 226 (313)
..++||+|+.++.-.....+++.+.+.++++|....++. +.-++++. ..+. ..+|.+|+.++.....+.-..+.
T Consensus 61 ~~~~Ig~i~~~~~~~~~~~~~~~i~~~~~~~gy~~~~~~-~~~~~~~~~~~~~~l~~~~vdgiIi~~~~~~~~~~l~~~~ 139 (315)
T PRK09492 61 SDKVVGIIVSRLDSLSENQAVRTMLPAFYEQGYDPIIME-SQFSPEKVNEHLGVLKRRNVDGVILFGFTGITEEMLAPWQ 139 (315)
T ss_pred CCCeEEEEecCCcCcccHHHHHHHHHHHHHcCCeEEEEe-cCCChHHHHHHHHHHHhcCCCEEEEeCCCcccHHHHHhcC
Confidence 457899999988777888999999999999997764433 33344332 2221 14999999875322233333445
Q ss_pred Cccc
Q 042576 227 KPLL 230 (313)
Q Consensus 227 kPvL 230 (313)
+|++
T Consensus 140 ~pvv 143 (315)
T PRK09492 140 DKLV 143 (315)
T ss_pred CCEE
Confidence 5654
No 10
>cd01537 PBP1_Repressors_Sugar_Binding_like Ligand-binding domain of the LacI-GalR family of transcription regulators and the sugar-binding domain of ABC-type transport systems. Ligand-binding domain of the LacI-GalR family of transcription regulators and the sugar-binding domain of ABC-type transport systems, all of which contain the type I periplasmic binding protein-like fold. Their specific ligands include lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars. The LacI family of proteins consists of transcriptional regulators related to the lac repressor; in general the sugar binding domain in this family binds a sugar, which in turn changes the DNA binding activity of the repressor domain. The core structure of the periplasmic binding proteins is classified into two types and they differ in number and order of beta strands in each domain: type I, which has six beta strands, and type II, which has five beta strands. These two distinct structural arrangem
Probab=81.92 E-value=34 Score=29.76 Aligned_cols=130 Identities=16% Similarity=0.215 Sum_probs=62.6
Q ss_pred cHhHHHHHHHHHHhCCCeEEecCCCCCCCccccCCCCCCCCCCCCCCeEEEecCCcccHH-HHHhhCCCceEEEeCCCCC
Q 042576 48 FASAIRAAKPELEKQGFKVMIPQSKPLSAGEVLGCTAPKIPARESDFNLVFIADGRFHLE-AFMISNPGIKTFRYDPYLG 126 (313)
Q Consensus 48 f~~~l~~~~~~L~~~g~~v~ipq~~pls~GevLGCt~~~~~~~~~~d~iv~igdGrFHle-~~mi~np~~~~y~yDPys~ 126 (313)
+......+++.+++.|+++.+-.... .+.+..-+-...+. ..+|++|..+.....+. --.+.+...|++.+|-...
T Consensus 14 ~~~~~~g~~~~~~~~g~~l~~~~~~~-~~~~~~~~~~~~~~--~~~d~ii~~~~~~~~~~~~~~l~~~~ip~v~~~~~~~ 90 (264)
T cd01537 14 FAQVLKGIEEAAKAAGYQVLLANSQN-DAEKQLSALENLIA--RGVDGIIIAPSDLTAPTIVKLARKAGIPVVLVDRDIP 90 (264)
T ss_pred HHHHHHHHHHHHHHcCCeEEEEeCCC-CHHHHHHHHHHHHH--cCCCEEEEecCCCcchhHHHHhhhcCCCEEEeccCCC
Confidence 44455667777777777755421110 00000000000011 13677766543222222 1223445677777764432
Q ss_pred ---cccccccChHHHHHHHHHHHHHHh-hcCCEEEEEEeCCCCCCcHHHHHHHHHHHHHcC
Q 042576 127 ---KLFLEEYDNKGMRETRKRAIEKAM-KEARTWGIVLGTLGRQGNPRILERLQKRMEKKG 183 (313)
Q Consensus 127 ---~~~~e~~d~~~~l~~R~~~I~kak-~~A~~~GIIvgTLg~Q~~~~ii~~l~~ll~~~G 183 (313)
.+..-..|...+- ..+.+.++ ...+++|+|.+...........+-+++.+++.|
T Consensus 91 ~~~~~~~v~~d~~~~~---~~~~~~l~~~g~~~i~~i~~~~~~~~~~~~~~~~~~~~~~~~ 148 (264)
T cd01537 91 DGDRVPSVGSDNEQAG---YLAGEHLAEKGHRRIALLAGPLGSSTARERVAGFKDALKEAG 148 (264)
T ss_pred CCcccceEecCcHHHH---HHHHHHHHHhcCCcEEEEECCCCCCcHHHHHHHHHHHHHHcC
Confidence 2222223333222 12222322 036799999887664455566788888888887
No 11
>cd06320 PBP1_allose_binding Periplasmic allose-binding domain of bacterial transport systems that function as a primary receptor of active transport and chemotaxis. Periplasmic allose-binding domain of bacterial transport systems that function as a primary receptor of active transport and chemotaxis. The members of this group are belonging to a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily. Like other periplasmic receptors of the ABC-type transport systems, the allose-binding protein consists of two alpha/beta domains connected by a three-stranded hinge. This Venus flytrap-like domain undergoes transition from an open to a closed conformational state upon ligand binding.
Probab=79.99 E-value=45 Score=29.93 Aligned_cols=159 Identities=18% Similarity=0.139 Sum_probs=77.4
Q ss_pred cHhHHHHHHHHHHhCCCeEEecCCC-CCCCccccCCCCCCCCCCCCCCeEEEecCCcccH-HHH-HhhCCCceEEEeCCC
Q 042576 48 FASAIRAAKPELEKQGFKVMIPQSK-PLSAGEVLGCTAPKIPARESDFNLVFIADGRFHL-EAF-MISNPGIKTFRYDPY 124 (313)
Q Consensus 48 f~~~l~~~~~~L~~~g~~v~ipq~~-pls~GevLGCt~~~~~~~~~~d~iv~igdGrFHl-e~~-mi~np~~~~y~yDPy 124 (313)
|...++.+.+.++++|+++.+-... .-.+-....+--..+. ..+|++++.+...-.+ ..+ .+..-.+|+..+|..
T Consensus 14 ~~~~~~gi~~~~~~~g~~~~~~~~~~~~~~~~~~~~i~~l~~--~~vdgiIi~~~~~~~~~~~~~~~~~~~iPvV~~~~~ 91 (275)
T cd06320 14 WRSLKEGYENEAKKLGVSVDIQAAPSEGDQQGQLSIAENMIN--KGYKGLLFSPISDVNLVPAVERAKKKGIPVVNVNDK 91 (275)
T ss_pred HHHHHHHHHHHHHHhCCeEEEEccCCCCCHHHHHHHHHHHHH--hCCCEEEECCCChHHhHHHHHHHHHCCCeEEEECCC
Confidence 5555677888888889887651100 0000000000000011 1378887664321111 111 123346788888853
Q ss_pred CC--cccccccChHHHHH-HHHHHHHHHhhcCCEEEEEEeCCCCCCcHHHHHHHHHHHHHc-CCcEEEEEeCCCCHH---
Q 042576 125 LG--KLFLEEYDNKGMRE-TRKRAIEKAMKEARTWGIVLGTLGRQGNPRILERLQKRMEKK-GFDYVVIMMSEISPA--- 197 (313)
Q Consensus 125 s~--~~~~e~~d~~~~l~-~R~~~I~kak~~A~~~GIIvgTLg~Q~~~~ii~~l~~ll~~~-Gkk~y~i~v~einp~--- 197 (313)
.. .......|..+.-+ .=.+++++.. ..++++++.|.........-.+-+++.++++ |.+......++-+++
T Consensus 92 ~~~~~~~~V~~d~~~~g~~~~~~l~~~~~-g~~~i~~l~~~~~~~~~~~r~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~ 170 (275)
T cd06320 92 LIPNATAFVGTDNKANGVRGAEWIIDKLA-EGGKVAIIEGKAGAFAAEQRTEGFTEAIKKASGIEVVASQPADWDREKAY 170 (275)
T ss_pred CCCccceEEecCcHHHHHHHHHHHHHHhC-CCceEEEEeCCCCCccHHHHHHHHHHHHhhCCCcEEEEecCCCccHHHHH
Confidence 21 11112233332211 1122333433 4568999888665554455567788888988 877654444444442
Q ss_pred -----HHhcCcCCccEEE
Q 042576 198 -----RVALFEDSVDAWI 210 (313)
Q Consensus 198 -----KLanf~~~ID~fV 210 (313)
.|...+ ++|+++
T Consensus 171 ~~~~~~l~~~~-~~~ai~ 187 (275)
T cd06320 171 DVATTILQRNP-DLKAIY 187 (275)
T ss_pred HHHHHHHHhCC-CccEEE
Confidence 233445 577654
No 12
>PRK07188 nicotinate phosphoribosyltransferase; Provisional
Probab=78.08 E-value=6.8 Score=38.79 Aligned_cols=65 Identities=22% Similarity=0.392 Sum_probs=49.1
Q ss_pred HHHHHhh-cCCEEEEEEeCCCCC-------------------CcHHHHHHHHHHHHHcC-CcEEEEEeCCCCHHHHhcCc
Q 042576 145 AIEKAMK-EARTWGIVLGTLGRQ-------------------GNPRILERLQKRMEKKG-FDYVVIMMSEISPARVALFE 203 (313)
Q Consensus 145 ~I~kak~-~A~~~GIIvgTLg~Q-------------------~~~~ii~~l~~ll~~~G-kk~y~i~v~einp~KLanf~ 203 (313)
++.-|+. ..+.+||=+=|-|-| -.+++++++++.|.+.| .+.-+++.|.||+++++.|.
T Consensus 219 al~~a~~~g~~l~gVRlDs~gdl~DK~~~~~~~~~~~~~~~G~~~~l~~~vr~~Ld~~g~~~vkI~aSgGine~~I~~~~ 298 (352)
T PRK07188 219 SLKVAREFGDKLKGVRVDTSKNMIDKYFIRHPEVLGTFDPRGVNPELIKALRKALDENGGKHVKIIVSSGFDAKKIREFE 298 (352)
T ss_pred HHHHHHHhCCCccEEEeCCcchHhhhhcccccccccccccccccHHHHHHHHHHHhhCCCCCcEEEEeCCCCHHHHHHHH
Confidence 3344441 467889966663333 46899999999999999 77888999999999999995
Q ss_pred C---CccEE
Q 042576 204 D---SVDAW 209 (313)
Q Consensus 204 ~---~ID~f 209 (313)
. .||+|
T Consensus 299 ~~g~piD~~ 307 (352)
T PRK07188 299 AQNVPVDIY 307 (352)
T ss_pred HcCCCccEE
Confidence 2 27887
No 13
>cd01574 PBP1_LacI Ligand-binding domain of DNA transcription repressor LacI specific for lactose, a member of the LacI-GalR family of bacterial transcription regulators. Ligand-binding domain of DNA transcription repressor LacI specific for lactose, a member of the LacI-GalR family of bacterial transcription regulators. The ligand-binding domain of LacI is structurally homologous to the periplasmic sugar-binding domain of ABC-type transporters and both domains contain the type I periplasmic binding protein-like fold. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the type I periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA b
Probab=74.35 E-value=42 Score=29.76 Aligned_cols=143 Identities=12% Similarity=0.073 Sum_probs=66.6
Q ss_pred ccHhHHHHHHHHHHhCCCeEEecCCCCCCCccccCCCCCCCCCCCCCCeEEEecCCcccHHHHHhhCCCceEEEeCCCCC
Q 042576 47 QFASAIRAAKPELEKQGFKVMIPQSKPLSAGEVLGCTAPKIPARESDFNLVFIADGRFHLEAFMISNPGIKTFRYDPYLG 126 (313)
Q Consensus 47 Qf~~~l~~~~~~L~~~g~~v~ipq~~pls~GevLGCt~~~~~~~~~~d~iv~igdGrFHle~~mi~np~~~~y~yDPys~ 126 (313)
.|...++.+.+.+++.|+.+.+-......+.....+-..... ..+|++++.+...-...-.....-++|++.+|-...
T Consensus 13 ~~~~~~~gi~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~--~~vdgiii~~~~~~~~~~~~~~~~~ipvv~~~~~~~ 90 (264)
T cd01574 13 GPSSTLAAIESAAREAGYAVTLSMLAEADEEALRAAVRRLLA--QRVDGVIVNAPLDDADAALAAAPADVPVVFVDGSPS 90 (264)
T ss_pred cHHHHHHHHHHHHHHCCCeEEEEeCCCCchHHHHHHHHHHHh--cCCCEEEEeCCCCChHHHHHHHhcCCCEEEEeccCC
Confidence 345556777778887788765411100000000000000001 236887766542211111111223577777774321
Q ss_pred -cccccccCh---HHHHHHHHHHHHHHhhcCCEEEEEEeCCCCCCcHHHHHHHHHHHHHcCCcEEEEEeCCCCH
Q 042576 127 -KLFLEEYDN---KGMRETRKRAIEKAMKEARTWGIVLGTLGRQGNPRILERLQKRMEKKGFDYVVIMMSEISP 196 (313)
Q Consensus 127 -~~~~e~~d~---~~~l~~R~~~I~kak~~A~~~GIIvgTLg~Q~~~~ii~~l~~ll~~~Gkk~y~i~v~einp 196 (313)
.+.....|. .++...+. ++ + ..+++++|.|..+......-.+-.++-+++.|.+......+..+.
T Consensus 91 ~~~~~v~~d~~~~g~~~~~~l--~~--~-g~~~i~~i~~~~~~~~~~~r~~gf~~~l~~~~~~~~~~~~~~~~~ 159 (264)
T cd01574 91 PRVSTVSVDQEGGARLATEHL--LE--L-GHRTIAHVAGPEEWLSARARLAGWRAALEAAGIAPPPVLEGDWSA 159 (264)
T ss_pred CCCCEEEeCcHHHHHHHHHHH--HH--C-CCCEEEEEecCCccchHHHHHHHHHHHHHHCCCCcceeeecCCCH
Confidence 122222232 22222221 11 4 567899998876644444555567777777787654444444443
No 14
>cd06280 PBP1_LacI_like_4 Ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. This group includes the ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.
Probab=72.23 E-value=14 Score=33.10 Aligned_cols=60 Identities=13% Similarity=0.252 Sum_probs=45.3
Q ss_pred EEEEEEeCCCCCCcHHHHHHHHHHHHHcCCcEEEEEeCCCCHHHHhc----C-cCCccEEEEecCC
Q 042576 155 TWGIVLGTLGRQGNPRILERLQKRMEKKGFDYVVIMMSEISPARVAL----F-EDSVDAWIQIACP 215 (313)
Q Consensus 155 ~~GIIvgTLg~Q~~~~ii~~l~~ll~~~Gkk~y~i~v~einp~KLan----f-~~~ID~fV~iaCP 215 (313)
+||+|+..+....+..+++.+++.+++.|.+.. +..++-++++... + ...+|++|+.+|.
T Consensus 1 ~Ig~i~p~~~~~~~~~~~~~i~~~~~~~g~~~~-~~~~~~~~~~~~~~i~~l~~~~~dgiii~~~~ 65 (263)
T cd06280 1 TVGLIVADIRNPFFTAVSRAVEDAAYRAGLRVI-LCNTDEDPEKEAMYLELMEEERVTGVIFAPTR 65 (263)
T ss_pred CEEEEecccccccHHHHHHHHHHHHHHCCCEEE-EEeCCCCHHHHHHHHHHHHhCCCCEEEEeCCC
Confidence 489999999888999999999999999997764 4444556654322 2 1149999998874
No 15
>cd06289 PBP1_MalI_like Ligand-binding domain of MalI, a transcription regulator of the maltose system of Escherichia coli and its close homologs from other bacteria. This group includes the ligand-binding domain of MalI, a transcription regulator of the maltose system of Escherichia coli and its close homologs from other bacteria. They are members of the LacI-GalR family of repressor proteins which are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.
Probab=71.73 E-value=10 Score=33.70 Aligned_cols=76 Identities=17% Similarity=0.146 Sum_probs=49.2
Q ss_pred EEEEEEeCCCCCCcHHHHHHHHHHHHHcCCcEEEEEeCCCCHHHHh----cCc-CCccEEEEecCCCccc---cccCCCC
Q 042576 155 TWGIVLGTLGRQGNPRILERLQKRMEKKGFDYVVIMMSEISPARVA----LFE-DSVDAWIQIACPRLSI---DWGDAFT 226 (313)
Q Consensus 155 ~~GIIvgTLg~Q~~~~ii~~l~~ll~~~Gkk~y~i~v~einp~KLa----nf~-~~ID~fV~iaCPrlsi---d~~~~f~ 226 (313)
++|+|+....-..+..+++.+++.+++.|.+..++ .+.-++++.. ++. ..+|+++..+|...+. .....-.
T Consensus 1 ~I~vi~~~~~~~~~~~~~~g~~~~a~~~g~~~~~~-~~~~~~~~~~~~i~~~~~~~vdgiii~~~~~~~~~~~~~~~~~~ 79 (268)
T cd06289 1 TIGLVINDLTNPFFAELAAGLEEVLEEAGYTVFLA-NSGEDVERQEQLLSTMLEHGVAGIILCPAAGTSPDLLKRLAESG 79 (268)
T ss_pred CEEEEecCCCcchHHHHHHHHHHHHHHcCCeEEEe-cCCCChHHHHHHHHHHHHcCCCEEEEeCCCCccHHHHHHHHhcC
Confidence 47889888877778888899999999988765433 4445555422 221 1489999988865432 2223334
Q ss_pred CcccC
Q 042576 227 KPLLT 231 (313)
Q Consensus 227 kPvLT 231 (313)
.|+++
T Consensus 80 ipvV~ 84 (268)
T cd06289 80 IPVVL 84 (268)
T ss_pred CCEEE
Confidence 56654
No 16
>cd06313 PBP1_ABC_sugar_binding_like_5 Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems. Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily, which consists of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis.
Probab=71.68 E-value=78 Score=28.64 Aligned_cols=146 Identities=14% Similarity=0.019 Sum_probs=70.7
Q ss_pred ccHhHHHHHHHHHHhCCCeEEecCCCCCCCccccCCCCCCCCCCCCCCeEEEecCCc-ccHHHH-HhhCCCceEEEeCCC
Q 042576 47 QFASAIRAAKPELEKQGFKVMIPQSKPLSAGEVLGCTAPKIPARESDFNLVFIADGR-FHLEAF-MISNPGIKTFRYDPY 124 (313)
Q Consensus 47 Qf~~~l~~~~~~L~~~g~~v~ipq~~pls~GevLGCt~~~~~~~~~~d~iv~igdGr-FHle~~-mi~np~~~~y~yDPy 124 (313)
-|...++.+.+.+++.|+++++-.... .+......-...+. ..+|++++.+.+. .....+ .+....+|+..+|..
T Consensus 13 f~~~~~~gi~~~~~~~G~~~~~~~~~~-d~~~~~~~i~~~~~--~~vdgiii~~~~~~~~~~~i~~~~~~~iPvV~~~~~ 89 (272)
T cd06313 13 WCAQGKQAADEAGKLLGVDVTWYGGAL-DAVKQVAAIENMAS--QGWDFIAVDPLGIGTLTEAVQKAIARGIPVIDMGTL 89 (272)
T ss_pred HHHHHHHHHHHHHHHcCCEEEEecCCC-CHHHHHHHHHHHHH--cCCCEEEEcCCChHHhHHHHHHHHHCCCcEEEeCCC
Confidence 455556778888888899876522110 00000000000011 2368887765321 111111 122347788888853
Q ss_pred CC----c-ccccccChHHHH-HHHHHHHHHHhhcCCEEEEEEeCCCCCCcHHHHHHHHHHHHHcC-CcEEEEEeCCCCH
Q 042576 125 LG----K-LFLEEYDNKGMR-ETRKRAIEKAMKEARTWGIVLGTLGRQGNPRILERLQKRMEKKG-FDYVVIMMSEISP 196 (313)
Q Consensus 125 s~----~-~~~e~~d~~~~l-~~R~~~I~kak~~A~~~GIIvgTLg~Q~~~~ii~~l~~ll~~~G-kk~y~i~v~einp 196 (313)
.. . ......|..+.- ..=.+++++.. ..+++++|-|..+......-.+-.++-++++| .+...+..+.-+.
T Consensus 90 ~~~~~~~~~~~v~~d~~~~g~~~~~~l~~~~~-g~~~i~~l~g~~~~~~~~~R~~gf~~~~~~~~~~~~~~~~~~~~~~ 167 (272)
T cd06313 90 IAPLQINVHSFLAPDNYFMGASVAQALCNAMG-GKGKIAMLQGALGHTGAQGRAQGFNDVIKKYPDIEVVDEQPANWDV 167 (272)
T ss_pred CCCCCCceEEEECCCcHHHHHHHHHHHHHHcC-CCceEEEEECCCCCcchhHHHHHHHHHHHhCCCCEEEeccCCCCCH
Confidence 21 1 211223332221 11133444545 66789999887765544455566677777776 4433223344443
No 17
>TIGR02417 fruct_sucro_rep D-fructose-responsive transcription factor. Members of this family belong the lacI helix-turn-helix family (pfam00356) of DNA-binding transcriptional regulators. All members are from the proteobacteria. Characterized members act as positive and negative transcriptional regulators of fructose and sucrose transport and metabolism. Sucrose is a disaccharide composed of fructose and glucose; D-fructose-1-phosphate rather than an intact sucrose moiety has been shown to act as the inducer.
Probab=71.37 E-value=44 Score=31.10 Aligned_cols=151 Identities=11% Similarity=0.089 Sum_probs=73.7
Q ss_pred eEEEEe-cc---ccHhHHHHHHHHHHhCCCeEEecCCCCCCCccccCCCCCCCCCCCCCCeEEEecCCc-ccHHHHHhhC
Q 042576 39 KLILAG-TI---QFASAIRAAKPELEKQGFKVMIPQSKPLSAGEVLGCTAPKIPARESDFNLVFIADGR-FHLEAFMISN 113 (313)
Q Consensus 39 ~i~Lv~-ti---Qf~~~l~~~~~~L~~~g~~v~ipq~~pls~GevLGCt~~~~~~~~~~d~iv~igdGr-FHle~~mi~n 113 (313)
.|+++. ++ -|...++.+.+.+++.|+.+++-.... .+.+....-..... ..+|++|+.+... ....--.+..
T Consensus 62 ~Igvi~~~~~~~~~~~~~~~i~~~~~~~gy~~~i~~~~~-~~~~~~~~~~~l~~--~~vdgiIi~~~~~~~~~~~~~l~~ 138 (327)
T TIGR02417 62 TIGLVIPDLENYSYARIAKELEQQCREAGYQLLIACSDD-NPDQEKVVIENLLA--RQVDALIVASCMPPEDAYYQKLQN 138 (327)
T ss_pred eEEEEeCCCCCccHHHHHHHHHHHHHHCCCEEEEEeCCC-CHHHHHHHHHHHHH--cCCCEEEEeCCCCCChHHHHHHHh
Confidence 577664 22 355567778889999999977632211 11100000000001 2378888775322 1211122344
Q ss_pred CCceEEEeCCCCC--cccccccChHHHHHHHHHHHHHHh-hcCCEEEEEEeCCCCCCcHHHHHHHHHHHHHcCCcEEEEE
Q 042576 114 PGIKTFRYDPYLG--KLFLEEYDNKGMRETRKRAIEKAM-KEARTWGIVLGTLGRQGNPRILERLQKRMEKKGFDYVVIM 190 (313)
Q Consensus 114 p~~~~y~yDPys~--~~~~e~~d~~~~l~~R~~~I~kak-~~A~~~GIIvgTLg~Q~~~~ii~~l~~ll~~~Gkk~y~i~ 190 (313)
..+|++.+|.... .+.....|... .-+ .+++... ...++||+|.|....+....-.+-.++-++++|.+...+.
T Consensus 139 ~~iPvV~~~~~~~~~~~~~V~~dn~~--~~~-~~~~~L~~~G~~~I~~i~~~~~~~~~~~R~~Gf~~al~~~~~~~~~~~ 215 (327)
T TIGR02417 139 EGLPVVALDRSLDDEHFCSVISDDVD--AAA-ELIERLLSQHADEFWYLGAQPELSVSRDRLAGFRQALKQATLEVEWVY 215 (327)
T ss_pred cCCCEEEEccccCCCCCCEEEeCcHH--HHH-HHHHHHHHCCCCeEEEEeCcccchhHHHHHHHHHHHHHHcCCChHhEE
Confidence 5788888885422 12212223222 112 1222222 1567999997765433333444556677788886543333
Q ss_pred eCCCC
Q 042576 191 MSEIS 195 (313)
Q Consensus 191 v~ein 195 (313)
.+..+
T Consensus 216 ~~~~~ 220 (327)
T TIGR02417 216 GGNYS 220 (327)
T ss_pred eCCCC
Confidence 34444
No 18
>cd06287 PBP1_LacI_like_8 Ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. This group includes the ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.
Probab=70.63 E-value=85 Score=28.60 Aligned_cols=127 Identities=11% Similarity=0.094 Sum_probs=71.0
Q ss_pred ccHhHHHHHHHHHHhCCCeEEecCCCCCCCccccCCCCCCCCCCCCCCeEEEecCCcccHHHH-HhhCCCceEEEeCCCC
Q 042576 47 QFASAIRAAKPELEKQGFKVMIPQSKPLSAGEVLGCTAPKIPARESDFNLVFIADGRFHLEAF-MISNPGIKTFRYDPYL 125 (313)
Q Consensus 47 Qf~~~l~~~~~~L~~~g~~v~ipq~~pls~GevLGCt~~~~~~~~~~d~iv~igdGrFHle~~-mi~np~~~~y~yDPys 125 (313)
-|...++.+.+.++++|+.+++-.... .-+ .+.. ..+|++|+++.. .....+ .+..-..|++.+|...
T Consensus 21 ~~~~~~~~i~~~~~~~gy~~~~~~~~~--~~~-------~l~~-~~vdgiIi~~~~-~~~~~~~~l~~~~iPvV~i~~~~ 89 (269)
T cd06287 21 FMMEVAAAAAESALERGLALCLVPPHE--ADS-------PLDA-LDIDGAILVEPM-ADDPQVARLRQRGIPVVSIGRPP 89 (269)
T ss_pred cHHHHHHHHHHHHHHCCCEEEEEeCCC--chh-------hhhc-cCcCeEEEecCC-CCCHHHHHHHHcCCCEEEeCCCC
Confidence 456778889999999999987643321 001 1111 247998887533 121211 2344467888887543
Q ss_pred ---CcccccccChHHHHHHHHHHHHHHh-hcCCEEEEEEeCCCCCCcHHHHHHHHHHHHHcCCcEE
Q 042576 126 ---GKLFLEEYDNKGMRETRKRAIEKAM-KEARTWGIVLGTLGRQGNPRILERLQKRMEKKGFDYV 187 (313)
Q Consensus 126 ---~~~~~e~~d~~~~l~~R~~~I~kak-~~A~~~GIIvgTLg~Q~~~~ii~~l~~ll~~~Gkk~y 187 (313)
..+.....|..+.- +.+++... ...+++|+|.|+.......+-.+-.++-++++|....
T Consensus 90 ~~~~~~~~V~~d~~~~~---~~a~~~L~~~G~~~I~~i~~~~~~~~~~~R~~gf~~a~~~~g~~~~ 152 (269)
T cd06287 90 GDRTDVPYVDLQSAATA---RMLLEHLRAQGARQIALIVGSARRNSYLEAEAAYRAFAAEHGMPPV 152 (269)
T ss_pred CCCCCCCeEeeCcHHHH---HHHHHHHHHcCCCcEEEEeCCcccccHHHHHHHHHHHHHHcCCCcc
Confidence 12322334433321 11222222 1467999998876544444455667788888887653
No 19
>TIGR02990 ectoine_eutA ectoine utilization protein EutA. Members of this protein family are EutA, a predicted arylmalonate decarboxylase found in a conserved ectoine utilization operon of species that include Sinorhizobium meliloti 1021 (where it is known to be induced by ectoine), Mesorhizobium loti and Silicibacter pomeroyi. It is missing from two other species with the other ectoine transport and utilization genes: Pseudomonas putida and Agrobacterium tumefaciens.
Probab=70.52 E-value=11 Score=35.18 Aligned_cols=82 Identities=23% Similarity=0.358 Sum_probs=61.8
Q ss_pred HHhhcCCEEEEEEeCCCCCCcHHHHHHHHHHHHHcCCcEEEE---------EeCCCCHHHHhcC-----cCCccEEEEec
Q 042576 148 KAMKEARTWGIVLGTLGRQGNPRILERLQKRMEKKGFDYVVI---------MMSEISPARVALF-----EDSVDAWIQIA 213 (313)
Q Consensus 148 kak~~A~~~GIIvgTLg~Q~~~~ii~~l~~ll~~~Gkk~y~i---------~v~einp~KLanf-----~~~ID~fV~ia 213 (313)
++. ++++++|+- -+..++-+++++-++++|.++.-+ -++++.|+-+..+ ..+.|+.++ +
T Consensus 116 ~al-g~~RIalvT-----PY~~~v~~~~~~~l~~~G~eV~~~~~~~~~~~~~ia~i~p~~i~~~~~~~~~~~aDAifi-s 188 (239)
T TIGR02990 116 AAL-GVRRISLLT-----PYTPETSRPMAQYFAVRGFEIVNFTCLGLTDDREMARISPDCIVEAALAAFDPDADALFL-S 188 (239)
T ss_pred HHc-CCCEEEEEC-----CCcHHHHHHHHHHHHhCCcEEeeeeccCCCCCceeeecCHHHHHHHHHHhcCCCCCEEEE-e
Confidence 556 889999885 578889999999999999998776 4667888886643 126888655 4
Q ss_pred CCCccccc-----cCCCCCcccCHHHHH
Q 042576 214 CPRLSIDW-----GDAFTKPLLTPFEAE 236 (313)
Q Consensus 214 CPrlsid~-----~~~f~kPvLTPyE~~ 236 (313)
|=-+...+ ..++-|||||.--+.
T Consensus 189 CTnLrt~~vi~~lE~~lGkPVlsSNqat 216 (239)
T TIGR02990 189 CTALRAATCAQRIEQAIGKPVVTSNQAT 216 (239)
T ss_pred CCCchhHHHHHHHHHHHCCCEEEHHHHH
Confidence 98874322 356889999876544
No 20
>PRK05569 flavodoxin; Provisional
Probab=70.36 E-value=23 Score=29.23 Aligned_cols=56 Identities=11% Similarity=0.163 Sum_probs=42.0
Q ss_pred EEEEEEeCCCCCCcHHHHHHHHHHHHHcCCcEEEEEeCCCCHHHHhcCcCCccEEEEecCCC
Q 042576 155 TWGIVLGTLGRQGNPRILERLQKRMEKKGFDYVVIMMSEISPARVALFEDSVDAWIQIACPR 216 (313)
Q Consensus 155 ~~GIIvgTLg~Q~~~~ii~~l~~ll~~~Gkk~y~i~v~einp~KLanf~~~ID~fV~iaCPr 216 (313)
++.||-+|. --+...+++.|.+.+++.|.++-++-+.+..+.++.+ .|+ |.++||=
T Consensus 3 ki~iiY~S~-tGnT~~iA~~i~~~~~~~g~~v~~~~~~~~~~~~~~~----~d~-iilgsPt 58 (141)
T PRK05569 3 KVSIIYWSC-GGNVEVLANTIADGAKEAGAEVTIKHVADAKVEDVLE----ADA-VAFGSPS 58 (141)
T ss_pred eEEEEEECC-CCHHHHHHHHHHHHHHhCCCeEEEEECCcCCHHHHhh----CCE-EEEECCC
Confidence 577888884 3455779999999999999888888888877765544 444 6677774
No 21
>cd06270 PBP1_GalS_like Ligand binding domain of DNA transcription iso-repressor GalS, which is one of two regulatory proteins involved in galactose transport and metabolism. Ligand binding domain of DNA transcription iso-repressor GalS, which is one of two regulatory proteins involved in galactose transport and metabolism. Transcription of the galactose regulon genes is regulated by Gal iso-repressor (GalS) and Gal repressor (GalR) in different ways, but both repressors recognize the same DNA binding site in the absence of D-galactose. GalS is a dimeric protein like GalR,and its major role is in regulating expression of the high-affinity galactose transporter encoded by the mgl operon, whereas GalR is the exclusive regulator of galactose permease, the low-affinity galactose transporter. GalS and GalR are members of the LacI-GalR family of transcription regulators and both contain the type I periplasmic binding protein-like fold. Hence, they are homologous to the periplasmic sugar bindi
Probab=70.32 E-value=80 Score=28.15 Aligned_cols=144 Identities=10% Similarity=0.085 Sum_probs=68.5
Q ss_pred ccHhHHHHHHHHHHhCCCeEEecCCCCCCCccccCCCCCCCCCCCCCCeEEEecCCcccHHHH-HhhCCCceEEEeCCCC
Q 042576 47 QFASAIRAAKPELEKQGFKVMIPQSKPLSAGEVLGCTAPKIPARESDFNLVFIADGRFHLEAF-MISNPGIKTFRYDPYL 125 (313)
Q Consensus 47 Qf~~~l~~~~~~L~~~g~~v~ipq~~pls~GevLGCt~~~~~~~~~~d~iv~igdGrFHle~~-mi~np~~~~y~yDPys 125 (313)
-|...++.+.+.+++.|+.+.+.....-...| ..+--.... ..+|++++.+.. .....+ .+..-++|++.+|-..
T Consensus 13 ~~~~~~~g~~~~a~~~g~~~~~~~~~~~~~~~-~~~i~~~~~--~~vdgii~~~~~-~~~~~~~~~~~~~ipvV~~~~~~ 88 (268)
T cd06270 13 FFGPLLSGVESVARKAGKHLIITAGHHSAEKE-REAIEFLLE--RRCDALILHSKA-LSDDELIELAAQVPPLVLINRHI 88 (268)
T ss_pred chHHHHHHHHHHHHHCCCEEEEEeCCCchHHH-HHHHHHHHH--cCCCEEEEecCC-CCHHHHHHHhhCCCCEEEEeccC
Confidence 45566677888888888886542110000000 000000001 237888887642 121111 1222356777776432
Q ss_pred C--cccccccChHHHHHHHHHHHHHHhhcCCEEEEEEeCCCCCCcHHHHHHHHHHHHHcCCcE--EEEEeCCCCH
Q 042576 126 G--KLFLEEYDNKGMRETRKRAIEKAMKEARTWGIVLGTLGRQGNPRILERLQKRMEKKGFDY--VVIMMSEISP 196 (313)
Q Consensus 126 ~--~~~~e~~d~~~~l~~R~~~I~kak~~A~~~GIIvgTLg~Q~~~~ii~~l~~ll~~~Gkk~--y~i~v~einp 196 (313)
. .......|..+.-+.=-..+ ..+ ..+++++|.|..+......-.+-+++-++++|.+. ..+..++.+.
T Consensus 89 ~~~~~~~v~~d~~~~~~~~~~~l-~~~-g~~~i~~i~~~~~~~~~~~R~~gf~~~~~~~~~~~~~~~~~~~~~~~ 161 (268)
T cd06270 89 PGLADRCIWLDNEQGGYLATEHL-IEL-GHRKIACITGPLTKEDARLRLQGYRDALAEAGIALDESLIIEGDFTE 161 (268)
T ss_pred CCCCCCeEEECcHHHHHHHHHHH-HHC-CCceEEEEeCCcccccHHHHHHHHHHHHHHcCCCCCcceEEECCCCH
Confidence 1 11111233333222111111 224 66789999887654433344555677888888764 3444455443
No 22
>cd01536 PBP1_ABC_sugar_binding_like Periplasmic sugar-binding domain of active transport systems that are members of the type I periplasmic binding protein (PBP1) superfamily. Periplasmic sugar-binding domain of active transport systems that are members of the type I periplasmic binding protein (PBP1) superfamily. The members of this family function as the primary receptors for chemotaxis and transport of many sugar based solutes in bacteria and archaea. The sugar binding domain is also homologous to the ligand-binding domain of eukaryotic receptors such as glutamate receptor (GluR) and DNA-binding transcriptional repressors such as LacI and GalR. Moreover, this periplasmic binding domain, also known as Venus flytrap domain, undergoes transition from an open to a closed conformational state upon the binding of ligands such as lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars. This family also includes the periplasmic binding domain of autoinducer-2 (AI-2
Probab=70.09 E-value=8.9 Score=33.81 Aligned_cols=60 Identities=13% Similarity=0.162 Sum_probs=31.8
Q ss_pred EEEEEEeCCCCCCcHHHHHHHHHHHHHcCCcEEEEEeCCCCHHHHh----cC-cCCccEEEEecCC
Q 042576 155 TWGIVLGTLGRQGNPRILERLQKRMEKKGFDYVVIMMSEISPARVA----LF-EDSVDAWIQIACP 215 (313)
Q Consensus 155 ~~GIIvgTLg~Q~~~~ii~~l~~ll~~~Gkk~y~i~v~einp~KLa----nf-~~~ID~fV~iaCP 215 (313)
+||+|+.......+..+++.+++.++++|.+..++-... ++++.. .+ ...+|++|..++.
T Consensus 1 ~ig~i~p~~~~~~~~~~~~~~~~~a~~~g~~~~~~~~~~-~~~~~~~~~~~l~~~~vdgvi~~~~~ 65 (267)
T cd01536 1 KIGLVVPSLNNPFWQAMNKGAEAAAKELGVELIVLDAQN-DVSKQIQQIEDLIAQGVDGIIISPVD 65 (267)
T ss_pred CEEEEeccccCHHHHHHHHHHHHHHHhcCceEEEECCCC-CHHHHHHHHHHHHHcCCCEEEEeCCC
Confidence 366666555555566677777777766665554443332 443211 11 1136666666554
No 23
>cd06301 PBP1_rhizopine_binding_like Periplasmic binding proteins specific to rhizopines. Periplasmic binding proteins specific to rhizopines, which are simple sugar-like compounds produced in the nodules induced by the symbiotic root nodule bacteria, such as Rhizobium and Sinorhizobium. Rhizopine-binding-like proteins from other bacteria are also included. Two inositol based rhizopine compounds are known to date: L-3-O-methly-scyllo-inosamine (3-O-MSI) and scyllo-inosamine. Bacterial strains that can metabolize rhizopine have a greater competitive advantage in nodulation and rhizopine synthesis is regulated by NifA/NtrA regulatory transcription activators which are maximally expressed at the onset of nitrogen fixation in bacteroids. The members of this group belong to the pentose/hexose sugar-binding protein family of the type I periplasmic binding protein superfamily.
Probab=69.44 E-value=83 Score=28.03 Aligned_cols=133 Identities=11% Similarity=0.052 Sum_probs=63.9
Q ss_pred ccHhHHHHHHHHHHh-CCCeEEecCCCCCCCccccCCCCCCCCCCCCCCeEEEecCC-cccHHH-HHhhCCCceEEEeCC
Q 042576 47 QFASAIRAAKPELEK-QGFKVMIPQSKPLSAGEVLGCTAPKIPARESDFNLVFIADG-RFHLEA-FMISNPGIKTFRYDP 123 (313)
Q Consensus 47 Qf~~~l~~~~~~L~~-~g~~v~ipq~~pls~GevLGCt~~~~~~~~~~d~iv~igdG-rFHle~-~mi~np~~~~y~yDP 123 (313)
.|...++.+.+.+++ .|+++++.... ..+.+...+--..+. ..+|+++..+.. ..+... -.+....+|++.+|-
T Consensus 13 ~~~~~~~gi~~~~~~~~~~~~~~~~~~-~~~~~~~~~i~~l~~--~~vdgiii~~~~~~~~~~~~~~l~~~~iPvv~~~~ 89 (272)
T cd06301 13 FLTLLRNAMKEHAKVLGGVELQFEDAK-NDVATQLSQVENFIA--QGVDAIIVVPVDTAATAPIVKAANAAGIPLVYVNR 89 (272)
T ss_pred HHHHHHHHHHHHHHHcCCcEEEEeCCC-CCHHHHHHHHHHHHH--cCCCEEEEecCchhhhHHHHHHHHHCCCeEEEecC
Confidence 344445667778888 78887653211 001011100000001 136887765432 112221 223445778888774
Q ss_pred CC----CcccccccChHHHHHHH-HHHHHHHhhcCCEEEEEEeCCCCCCcHHHHHHHHHHHHHcC
Q 042576 124 YL----GKLFLEEYDNKGMRETR-KRAIEKAMKEARTWGIVLGTLGRQGNPRILERLQKRMEKKG 183 (313)
Q Consensus 124 ys----~~~~~e~~d~~~~l~~R-~~~I~kak~~A~~~GIIvgTLg~Q~~~~ii~~l~~ll~~~G 183 (313)
.. ..+.....|....-+.= ..+++++. ..+++++|-|+........-.+-.++-++++|
T Consensus 90 ~~~~~~~~~~~V~~d~~~~g~~~~~~l~~~~~-~~~~i~~i~~~~~~~~~~~R~~gf~~~l~~~~ 153 (272)
T cd06301 90 RPENAPKGVAYVGSDEVVAGRLQAEYVADKLG-GKGNVAILMGPLGQSAQIDRTKGVEEVLAKYP 153 (272)
T ss_pred CCCCCCCeeEEEecChHHHHHHHHHHHHHHhC-CCccEEEEECCCCCccHHHHHHHHHHHHHHCC
Confidence 22 23333334433221111 22334434 44689998887654444444556677778877
No 24
>cd06274 PBP1_FruR Ligand binding domain of DNA transcription repressor specific for fructose (FruR) and its close homologs. Ligand binding domain of DNA transcription repressor specific for fructose (FruR) and its close homologs, all of which are a member of the LacI-GalR family of bacterial transcription regulators. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to members of the type I periplasmic binding protein superfamily. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor
Probab=68.87 E-value=16 Score=32.70 Aligned_cols=61 Identities=23% Similarity=0.370 Sum_probs=39.8
Q ss_pred EEEEEEeCCCCCCcHHHHHHHHHHHHHcCCcEEEEEeCCCCHHHHhc----C-cCCccEEEEecCCC
Q 042576 155 TWGIVLGTLGRQGNPRILERLQKRMEKKGFDYVVIMMSEISPARVAL----F-EDSVDAWIQIACPR 216 (313)
Q Consensus 155 ~~GIIvgTLg~Q~~~~ii~~l~~ll~~~Gkk~y~i~v~einp~KLan----f-~~~ID~fV~iaCPr 216 (313)
+||+|+..+....+..+++.+++.+++.|....++. ..-++++... + ...+|+.|..++..
T Consensus 1 ~igvi~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~-~~~~~~~~~~~i~~l~~~~vdgiii~~~~~ 66 (264)
T cd06274 1 TIGLIIPDLENRSFARIAKRLEALARERGYQLLIAC-SDDDPETERETVETLIARQVDALIVAGSLP 66 (264)
T ss_pred CEEEEeccccCchHHHHHHHHHHHHHHCCCEEEEEe-CCCCHHHHHHHHHHHHHcCCCEEEEcCCCC
Confidence 378888888777777888888888888877654433 3335544221 1 11388888877753
No 25
>PLN02925 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase
Probab=68.79 E-value=57 Score=35.31 Aligned_cols=144 Identities=17% Similarity=0.206 Sum_probs=82.9
Q ss_pred CChHHHHHHHHHhCCCCCeEEEE--eccccHhHHHHHHHHHHhCCCeEEecCCCCCCCccccCCCCCCCCCCCCCCeEEE
Q 042576 21 IDVNRLIDTIKVNYSDPGKLILA--GTIQFASAIRAAKPELEKQGFKVMIPQSKPLSAGEVLGCTAPKIPARESDFNLVF 98 (313)
Q Consensus 21 iD~~~~i~~i~~~f~~~~~i~Lv--~tiQf~~~l~~~~~~L~~~g~~v~ipq~~pls~GevLGCt~~~~~~~~~~d~iv~ 98 (313)
-|++..++++++....+..|+=+ -+.+-+.++..|++.|...|+++ =.
T Consensus 107 ~D~eatv~Qi~~l~~aGceiVRvtv~~~~~A~al~~I~~~L~~~g~~i------------------------------PL 156 (733)
T PLN02925 107 KDVEATVDQVMRIADKGADIVRITVQGKKEADACFEIKNTLVQKGYNI------------------------------PL 156 (733)
T ss_pred ccHHHHHHHHHHHHHcCCCEEEEcCCCHHHHHhHHHHHHHHhhcCCCC------------------------------CE
Confidence 36677777777765544444322 23566666777777777766542 13
Q ss_pred ecCCcccHHHHHhhCCCceEEEeCCCCC----------cccccccCh--HHHHHHHHHHHHHHhhcCCEEEEEEeCCCCC
Q 042576 99 IADGRFHLEAFMISNPGIKTFRYDPYLG----------KLFLEEYDN--KGMRETRKRAIEKAMKEARTWGIVLGTLGRQ 166 (313)
Q Consensus 99 igdGrFHle~~mi~np~~~~y~yDPys~----------~~~~e~~d~--~~~l~~R~~~I~kak~~A~~~GIIvgTLg~Q 166 (313)
|+|-.|+..-++.+-....-+|.||=+- ..|+|+|.. +++..+-...|++|| +.+ +.|=+|+-.|.
T Consensus 157 VADIHF~~~~Al~a~~~vdkiRINPGN~~~~~k~F~~~eYtdeeY~~Ele~i~e~f~~~v~~ak-~~~-~~iRIGvN~GS 234 (733)
T PLN02925 157 VADIHFAPSVALRVAECFDKIRVNPGNFADRRAQFEKLEYTEDDYQKELEHIEEVFTPLVEKCK-KYG-RAMRIGTNHGS 234 (733)
T ss_pred EEecCCCHHHHHHHHHhcCCeEECCcccCCccccccccccchhhhhhhHHHHHHHHHHHHHHHH-HCC-CCEEEecCCcC
Confidence 5666777655555444567788888321 234455542 222333346888888 533 33445554444
Q ss_pred CcHHHHHH--------------HHHHHHHcCCcEEEEEeCCCCH
Q 042576 167 GNPRILER--------------LQKRMEKKGFDYVVIMMSEISP 196 (313)
Q Consensus 167 ~~~~ii~~--------------l~~ll~~~Gkk~y~i~v~einp 196 (313)
-...++++ --+++++.|..-++|+|--=|+
T Consensus 235 Ls~ri~~~yGdtp~gmVeSAle~~~i~e~~~f~diviS~KsSn~ 278 (733)
T PLN02925 235 LSDRIMSYYGDSPRGMVESAFEFARICRKLDYHNFVFSMKASNP 278 (733)
T ss_pred chHHHHHHhCCChHHHHHHHHHHHHHHHHCCCCcEEEEEEcCCh
Confidence 44444433 1345778888888888765554
No 26
>cd06277 PBP1_LacI_like_1 Ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. This group includes the ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.
Probab=68.54 E-value=17 Score=32.50 Aligned_cols=61 Identities=13% Similarity=0.252 Sum_probs=38.8
Q ss_pred EEEEEeC---CCCCCcHHHHHHHHHHHHHcCCcEEEEEeCCCCHHHHh----cC-cCCccEEEEecCCCc
Q 042576 156 WGIVLGT---LGRQGNPRILERLQKRMEKKGFDYVVIMMSEISPARVA----LF-EDSVDAWIQIACPRL 217 (313)
Q Consensus 156 ~GIIvgT---Lg~Q~~~~ii~~l~~ll~~~Gkk~y~i~v~einp~KLa----nf-~~~ID~fV~iaCPrl 217 (313)
||+|+.+ ++......+++.+++.+++.|.+..+...+. +.++.. .+ ...+|++|+.++...
T Consensus 2 vgv~~~~~~~~~~~~~~~~~~~i~~~~~~~g~~~~~~~~~~-~~~~~~~~~~~l~~~~vdgiii~~~~~~ 70 (268)
T cd06277 2 IGLIASKRILNSPAFYSEIYRAIEEEAKKYGYNLILKFVSD-EDEEEFELPSFLEDGKVDGIILLGGIST 70 (268)
T ss_pred eEEEEeccccccCCcHHHHHHHHHHHHHHcCCEEEEEeCCC-ChHHHHHHHHHHHHCCCCEEEEeCCCCh
Confidence 6888877 5667777788888888888887766655543 322111 11 114888888776543
No 27
>cd06273 PBP1_GntR_like_1 This group includes the ligand-binding domain of putative DNA transcription repressors which are highly similar to that of the repressor specific for gluconate (GntR), a member of the LacI-GalR family of bacterial transcription regulators. This group includes the ligand-binding domain of putative DNA transcription repressors which are highly similar to that of the repressor specific for gluconate (GntR), a member of the LacI-GalR family of bacterial transcription regulators. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational
Probab=68.47 E-value=86 Score=27.80 Aligned_cols=157 Identities=14% Similarity=0.156 Sum_probs=75.0
Q ss_pred ccHhHHHHHHHHHHhCCCeEEecCCCCCCCccccCCCCCCCCCCCCCCeEEEecCCcccHHHH-HhhCCCceEEEeCCCC
Q 042576 47 QFASAIRAAKPELEKQGFKVMIPQSKPLSAGEVLGCTAPKIPARESDFNLVFIADGRFHLEAF-MISNPGIKTFRYDPYL 125 (313)
Q Consensus 47 Qf~~~l~~~~~~L~~~g~~v~ipq~~pls~GevLGCt~~~~~~~~~~d~iv~igdGrFHle~~-mi~np~~~~y~yDPys 125 (313)
-|...+..+.+.+++.|+.+++.... -.+.+.....- .+.. ..+|++++++... ....+ .+....+|++.+|-..
T Consensus 13 ~~~~~~~~i~~~~~~~g~~~~~~~~~-~~~~~~~~~~~-~l~~-~~vdgiii~~~~~-~~~~~~~l~~~~iPvv~~~~~~ 88 (268)
T cd06273 13 IFARVIQAFQETLAAHGYTLLVASSG-YDLDREYAQAR-KLLE-RGVDGLALIGLDH-SPALLDLLARRGVPYVATWNYS 88 (268)
T ss_pred hHHHHHHHHHHHHHHCCCEEEEecCC-CCHHHHHHHHH-HHHh-cCCCEEEEeCCCC-CHHHHHHHHhCCCCEEEEcCCC
Confidence 45556677888888889887652210 00110000000 0001 1378888776532 22211 2334567877776332
Q ss_pred C--cccccccChHHH---HHHHHHHHHHHhhcCCEEEEEEeCCCC-CCcHHHHHHHHHHHHHcCCcE--EEEEeCCCCHH
Q 042576 126 G--KLFLEEYDNKGM---RETRKRAIEKAMKEARTWGIVLGTLGR-QGNPRILERLQKRMEKKGFDY--VVIMMSEISPA 197 (313)
Q Consensus 126 ~--~~~~e~~d~~~~---l~~R~~~I~kak~~A~~~GIIvgTLg~-Q~~~~ii~~l~~ll~~~Gkk~--y~i~v~einp~ 197 (313)
. .+.....|..+. ...+ +++ + ..+++|+|-|.... .....-.+-.++.++++|.+. ..++.+..+.+
T Consensus 89 ~~~~~~~v~~d~~~~~~~~~~~--l~~--~-g~~~i~~i~~~~~~~~~~~~r~~gf~~~l~~~~~~~~~~~~~~~~~~~~ 163 (268)
T cd06273 89 PDSPYPCVGFDNREAGRLAARH--LIA--L-GHRRIAMIFGPTQGNDRARARRAGVRAALAEAGLELPELWQVEAPYSIA 163 (268)
T ss_pred CCCCCCEEEeChHHHHHHHHHH--HHH--C-CCCeEEEEeccccCCccHHHHHHHHHHHHHHcCCCCCHHHeeeCCCcHH
Confidence 1 111122232221 2111 122 4 67899999876532 223345666778888887442 22333344432
Q ss_pred -------H-HhcCcCCccEEEEec
Q 042576 198 -------R-VALFEDSVDAWIQIA 213 (313)
Q Consensus 198 -------K-Lanf~~~ID~fV~ia 213 (313)
+ |+.-+ ..|+++..+
T Consensus 164 ~~~~~~~~~l~~~~-~~~ai~~~~ 186 (268)
T cd06273 164 DGRAALRQLLEQPP-RPTAVICGN 186 (268)
T ss_pred HHHHHHHHHHcCCC-CCCEEEEcC
Confidence 2 22223 578877543
No 28
>PF00731 AIRC: AIR carboxylase; InterPro: IPR000031 Phosphoribosylaminoimidazole carboxylase is a fusion protein in plants and fungi, but consists of two non-interacting proteins in bacteria, PurK and PurE. PurK, N5-carboxyaminoimidazole ribonucleotide (N5_CAIR) synthetase, catalyzes the conversion of 5-aminoimidazole ribonucleotide (AIR), ATP, and bicarbonate to N5-CAIR, ADP, and Pi. PurE converts N5-CAIR to CAIR, the sixth step of de novo purine biosynthesis. In the presence of high concentrations of bicarbonate, PurE is reported able to convert AIR to CAIR directly and without ATP. Some members of this family contain two copies of this domain []. The crystal structure of PurE indicates a unique quaternary structure that confirms the octameric nature of the enzyme [].; GO: 0004638 phosphoribosylaminoimidazole carboxylase activity, 0006189 'de novo' IMP biosynthetic process; PDB: 3TRH_O 2YWX_A 2NSL_A 1D7A_A 2NSJ_A 1QCZ_A 2ATE_A 2NSH_A 3RG8_C 3RGG_D ....
Probab=68.09 E-value=20 Score=31.29 Aligned_cols=56 Identities=30% Similarity=0.463 Sum_probs=41.3
Q ss_pred EEEEEEeCCCCCCcHHHHHHHHHHHHHcCCcEEEEEeC-CCCHHHHhcC----c-CCccEEEEec
Q 042576 155 TWGIVLGTLGRQGNPRILERLQKRMEKKGFDYVVIMMS-EISPARVALF----E-DSVDAWIQIA 213 (313)
Q Consensus 155 ~~GIIvgTLg~Q~~~~ii~~l~~ll~~~Gkk~y~i~v~-einp~KLanf----~-~~ID~fV~ia 213 (313)
+++||.|+ .-...+++...+.|++-|+.+-+-+.| .-+|++|..| . .++|+||-+|
T Consensus 2 ~V~Ii~gs---~SD~~~~~~a~~~L~~~gi~~~~~V~saHR~p~~l~~~~~~~~~~~~~viIa~A 63 (150)
T PF00731_consen 2 KVAIIMGS---TSDLPIAEEAAKTLEEFGIPYEVRVASAHRTPERLLEFVKEYEARGADVIIAVA 63 (150)
T ss_dssp EEEEEESS---GGGHHHHHHHHHHHHHTT-EEEEEE--TTTSHHHHHHHHHHTTTTTESEEEEEE
T ss_pred eEEEEeCC---HHHHHHHHHHHHHHHHcCCCEEEEEEeccCCHHHHHHHHHHhccCCCEEEEEEC
Confidence 68899987 668899999999999999988776666 5578877766 2 1478887543
No 29
>COG0041 PurE Phosphoribosylcarboxyaminoimidazole (NCAIR) mutase [Nucleotide transport and metabolism]
Probab=67.86 E-value=20 Score=31.69 Aligned_cols=46 Identities=20% Similarity=0.424 Sum_probs=40.5
Q ss_pred EEEEEEeCCCCCCcHHHHHHHHHHHHHcCCcEEEEEeC-CCCHHHHhcCc
Q 042576 155 TWGIVLGTLGRQGNPRILERLQKRMEKKGFDYVVIMMS-EISPARVALFE 203 (313)
Q Consensus 155 ~~GIIvgTLg~Q~~~~ii~~l~~ll~~~Gkk~y~i~v~-einp~KLanf~ 203 (313)
.+|||+|+ +-.+++++..-+.|++-|..|-+-++| .=+|++|..|.
T Consensus 4 ~V~IIMGS---~SD~~~mk~Aa~~L~~fgi~ye~~VvSAHRTPe~m~~ya 50 (162)
T COG0041 4 KVGIIMGS---KSDWDTMKKAAEILEEFGVPYEVRVVSAHRTPEKMFEYA 50 (162)
T ss_pred eEEEEecC---cchHHHHHHHHHHHHHcCCCeEEEEEeccCCHHHHHHHH
Confidence 69999999 668999999999999999999876666 77999998884
No 30
>TIGR02405 trehalos_R_Ecol trehalose operon repressor, proteobacterial. This family consists of repressors of the LacI family typically associated with trehalose utilization operons. Trehalose is imported as trehalose-6-phosphate and then hydrolyzed by alpha,alpha-phosphotrehalase to glucose and glucose-6-P. This family includes repressors mostly from Gammaproteobacteria and does not include the GntR family TreR of Bacillus subtilis
Probab=67.68 E-value=28 Score=32.36 Aligned_cols=63 Identities=14% Similarity=0.302 Sum_probs=43.6
Q ss_pred cCCEEEEEEeCCCCCCcHHHHHHHHHHHHHcCCcEEEEEeCCCCHHHH----hcCc-CCccEEEEecCC
Q 042576 152 EARTWGIVLGTLGRQGNPRILERLQKRMEKKGFDYVVIMMSEISPARV----ALFE-DSVDAWIQIACP 215 (313)
Q Consensus 152 ~A~~~GIIvgTLg~Q~~~~ii~~l~~ll~~~Gkk~y~i~v~einp~KL----anf~-~~ID~fV~iaCP 215 (313)
..+++|+|+..+.--.+..+++.+.+.++++|....++ .+.-++++. ..+. ..+|.+|+++..
T Consensus 58 ~~~~Ig~i~~~~~~~~~~~~~~~i~~~~~~~gy~~~i~-~~~~~~~~~~~~~~~l~~~~vdGvIi~~~~ 125 (311)
T TIGR02405 58 SDKVVAVIVSRLDSPSENLAVSGMLPVFYTAGYDPIIM-ESQFSPQLTNEHLSVLQKRNVDGVILFGFT 125 (311)
T ss_pred CCCEEEEEeCCcccccHHHHHHHHHHHHHHCCCeEEEe-cCCCChHHHHHHHHHHHhcCCCEEEEeCCC
Confidence 45689999987765567789999999999999875444 344455442 2221 149999998653
No 31
>PRK06703 flavodoxin; Provisional
Probab=67.37 E-value=21 Score=30.10 Aligned_cols=55 Identities=11% Similarity=0.161 Sum_probs=41.5
Q ss_pred EEEEEEeCCCCCCcHHHHHHHHHHHHHcCCcEEEEEeCCCCHHHHhcCcCCccEEEEecCC
Q 042576 155 TWGIVLGTLGRQGNPRILERLQKRMEKKGFDYVVIMMSEISPARVALFEDSVDAWIQIACP 215 (313)
Q Consensus 155 ~~GIIvgTLg~Q~~~~ii~~l~~ll~~~Gkk~y~i~v~einp~KLanf~~~ID~fV~iaCP 215 (313)
++.|+.+|.. -+...+++.|.+.|.+.|.++-++-+.+..+..|.+ .|. |+++||
T Consensus 3 kv~IiY~S~t-GnT~~iA~~ia~~l~~~g~~v~~~~~~~~~~~~l~~----~d~-viigsp 57 (151)
T PRK06703 3 KILIAYASMS-GNTEDIADLIKVSLDAFDHEVVLQEMDGMDAEELLA----YDG-IILGSY 57 (151)
T ss_pred eEEEEEECCC-chHHHHHHHHHHHHHhcCCceEEEehhhCCHHHHhc----CCc-EEEEEC
Confidence 5789999943 445579999999999999999889888888776544 455 444555
No 32
>TIGR01753 flav_short flavodoxin, short chain. Flavodoxins are small redox-active proteins with a flavin mononucleotide (FMN) prosthetic group. They can act in nitrogen fixation by nitrogenase, in sulfite reduction, and light-dependent NADP+ reduction in during photosynthesis, among other roles. This model describes the short chain type. Many of these are involved in sulfite reduction.
Probab=67.03 E-value=22 Score=28.89 Aligned_cols=55 Identities=11% Similarity=0.265 Sum_probs=42.0
Q ss_pred EEEEEeCCCCCCcHHHHHHHHHHHHHcCCcEEEEEeCCCCHHHHhcCcCCccEEEEecCCC
Q 042576 156 WGIVLGTLGRQGNPRILERLQKRMEKKGFDYVVIMMSEISPARVALFEDSVDAWIQIACPR 216 (313)
Q Consensus 156 ~GIIvgTLg~Q~~~~ii~~l~~ll~~~Gkk~y~i~v~einp~KLanf~~~ID~fV~iaCPr 216 (313)
|-||.+|. --+...+++.|.+.+.+.|.++-++-+++.++.+|.. .|.+| +++|-
T Consensus 1 v~Iiy~S~-tGnT~~~A~~i~~~~~~~g~~v~~~~~~~~~~~~l~~----~d~ii-lgspt 55 (140)
T TIGR01753 1 ILIVYASM-TGNTEEMANIIAEGLKEAGAEVDLLEVADADAEDLLS----YDAVL-LGCST 55 (140)
T ss_pred CEEEEECC-CcHHHHHHHHHHHHHHhcCCeEEEEEcccCCHHHHhc----CCEEE-EEcCC
Confidence 35788885 3556679999999999999999999999999888755 45554 44443
No 33
>cd06293 PBP1_LacI_like_11 Ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. This group includes the ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.
Probab=66.83 E-value=21 Score=32.02 Aligned_cols=61 Identities=16% Similarity=0.307 Sum_probs=42.6
Q ss_pred EEEEEEeCCCCCCcHHHHHHHHHHHHHcCCcEEEEEeCCCCHHHHh----cCc-CCccEEEEecCCC
Q 042576 155 TWGIVLGTLGRQGNPRILERLQKRMEKKGFDYVVIMMSEISPARVA----LFE-DSVDAWIQIACPR 216 (313)
Q Consensus 155 ~~GIIvgTLg~Q~~~~ii~~l~~ll~~~Gkk~y~i~v~einp~KLa----nf~-~~ID~fV~iaCPr 216 (313)
+||+|+..++.-....+++.+.+.++++|....++... -++++.. .+. ..+|++|+.+|+-
T Consensus 1 ~Ig~i~~~~~~~~~~~~~~gi~~~~~~~gy~v~~~~~~-~~~~~~~~~i~~~~~~~~dgiii~~~~~ 66 (269)
T cd06293 1 TIGLVVPDIANPFFAELADAVEEEADARGLSLVLCATR-NRPERELTYLRWLDTNHVDGLIFVTNRP 66 (269)
T ss_pred CEEEEeCCCCCCcHHHHHHHHHHHHHHCCCEEEEEeCC-CCHHHHHHHHHHHHHCCCCEEEEeCCCC
Confidence 47999988876677789999999999999777555333 3554332 111 1489999988863
No 34
>PRK00694 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; Validated
Probab=66.80 E-value=70 Score=33.91 Aligned_cols=145 Identities=21% Similarity=0.216 Sum_probs=85.0
Q ss_pred CChHHHHHHHHHhCCCCCeEEEE--eccccHhHHHHHHHHHHhCCCeEEecCCCCCCCccccCCCCCCCCCCCCCCeEEE
Q 042576 21 IDVNRLIDTIKVNYSDPGKLILA--GTIQFASAIRAAKPELEKQGFKVMIPQSKPLSAGEVLGCTAPKIPARESDFNLVF 98 (313)
Q Consensus 21 iD~~~~i~~i~~~f~~~~~i~Lv--~tiQf~~~l~~~~~~L~~~g~~v~ipq~~pls~GevLGCt~~~~~~~~~~d~iv~ 98 (313)
-|++..++++++....+..|+=+ =+.+-+.++..|++.|+..|+++ | .
T Consensus 42 ~D~~atv~Qi~~L~~aGceiVRvtvp~~~~A~al~~I~~~L~~~g~~i------------------P------------L 91 (606)
T PRK00694 42 TDVDGTVRQICALQEWGCDIVRVTVQGLKEAQACEHIKERLIQQGISI------------------P------------L 91 (606)
T ss_pred ccHHHHHHHHHHHHHcCCCEEEEcCCCHHHHHhHHHHHHHHhccCCCC------------------C------------E
Confidence 47778888887766555444422 24577777888888888877652 1 2
Q ss_pred ecCCcccHHHHHhhCCCceEEEeCCCCC----------cccccccCh--HHHHHHHHHHHHHHhhcCCEEEEEEeCCCCC
Q 042576 99 IADGRFHLEAFMISNPGIKTFRYDPYLG----------KLFLEEYDN--KGMRETRKRAIEKAMKEARTWGIVLGTLGRQ 166 (313)
Q Consensus 99 igdGrFHle~~mi~np~~~~y~yDPys~----------~~~~e~~d~--~~~l~~R~~~I~kak~~A~~~GIIvgTLg~Q 166 (313)
|+|-.|....++.+-....-+|.||=+- ..|.|+|.. +++..+=...|++|| +. .+.|=+|+-.|.
T Consensus 92 VADIHF~~~~A~~a~~~vdkiRINPGNi~~~~k~F~~~~YtDeeY~~el~~I~e~~~~vV~~ak-e~-~~~IRIGvN~GS 169 (606)
T PRK00694 92 VADIHFFPQAAMHVADFVDKVRINPGNYVDKRNMFTGKIYTDEQYAHSLLRLEEKFSPLVEKCK-RL-GKAMRIGVNHGS 169 (606)
T ss_pred EeecCCChHHHHHHHHhcCceEECCcccCCccccccccccchhhhhhhhhhHHHHHHHHHHHHH-HC-CCCEEEecCCcC
Confidence 4555566555544434467778887321 234455542 333444466778887 43 334555555444
Q ss_pred CcHHHHHHH--------------HHHHHHcCCcEEEEEeCCCCHH
Q 042576 167 GNPRILERL--------------QKRMEKKGFDYVVIMMSEISPA 197 (313)
Q Consensus 167 ~~~~ii~~l--------------~~ll~~~Gkk~y~i~v~einp~ 197 (313)
-...++++. -+++++.|..-++|+|--=|+.
T Consensus 170 L~~~i~~~yG~tpegmVeSAle~~~i~e~~~f~diviS~KsSnv~ 214 (606)
T PRK00694 170 LSERVMQRYGDTIEGMVYSALEYIEVCEKLDYRDVVFSMKSSNPK 214 (606)
T ss_pred chHHHHHHhCCCHHHHHHHHHHHHHHHHHCCCCcEEEEEEcCCHH
Confidence 444444432 2456777877777777655553
No 35
>cd06354 PBP1_BmpA_PnrA_like Periplasmic binding domain of basic membrane lipoprotein, PnrA, in Treponema pallidum and its homologs from other bacteria and Archaea. Periplasmic binding domain of basic membrane lipoprotein, PnrA, in Treponema pallidum and its homologs from other bacteria and Archaea. The PnrA lipoprotein, also known as Tp0319 or TmpC, represents a novel family of bacterial purine nucleoside receptor encoded within an ATP-binding cassette (ABC) transport system (pnrABCDE). It shows a striking structural similarity to another basic membrane lipoprotein Med which regulates the competence transcription factor gene, comK, in Bacillus subtilis. The members of PnrA-like subgroup are likely to have similar nucleoside-binding functions and a similar type I periplasmic sugar-binding protein-like fold.
Probab=65.90 E-value=84 Score=28.51 Aligned_cols=129 Identities=10% Similarity=-0.068 Sum_probs=61.4
Q ss_pred ccHhHHHHHHHHHHhCCCeEEecCCC-CCCCccccCCCCCCCCCCCCCCeEEEecCCcccHH--HHHhhCCCceEEEeCC
Q 042576 47 QFASAIRAAKPELEKQGFKVMIPQSK-PLSAGEVLGCTAPKIPARESDFNLVFIADGRFHLE--AFMISNPGIKTFRYDP 123 (313)
Q Consensus 47 Qf~~~l~~~~~~L~~~g~~v~ipq~~-pls~GevLGCt~~~~~~~~~~d~iv~igdGrFHle--~~mi~np~~~~y~yDP 123 (313)
-|...++.+.+.+++.|+++++-... +-..-+.+ ..+.+ ..+|+++..+.. ++.. .+.-..+.+|+..+|-
T Consensus 16 f~~~~~~gi~~~~~~~gy~~~i~~~~~~~~~~~~i----~~l~~-~~vdgiI~~~~~-~~~~~~~~~~~~~~~PiV~i~~ 89 (265)
T cd06354 16 FNQSAWEGLERAAKELGIEYKYVESKSDADYEPNL----EQLAD-AGYDLIVGVGFL-LADALKEVAKQYPDQKFAIIDA 89 (265)
T ss_pred HHHHHHHHHHHHHHHcCCeEEEEecCCHHHHHHHH----HHHHh-CCCCEEEEcCcc-hHHHHHHHHHHCCCCEEEEEec
Confidence 45566777888888889887652211 10000000 00001 247888876533 2221 2222234678887764
Q ss_pred CC---CcccccccChHHHHHHHHHHHHHHhhcCCEEEEEEeCCCCCCcHHHHHHHHHHHHHcC
Q 042576 124 YL---GKLFLEEYDNKGMRETRKRAIEKAMKEARTWGIVLGTLGRQGNPRILERLQKRMEKKG 183 (313)
Q Consensus 124 ys---~~~~~e~~d~~~~l~~R~~~I~kak~~A~~~GIIvgTLg~Q~~~~ii~~l~~ll~~~G 183 (313)
.. ..+.....|....-..=-.++.+.. .-+++|+|.|+.. .......+-.++-++++|
T Consensus 90 ~~~~~~~~~~v~~d~~~a~~~a~~ll~~~~-G~~~I~~i~~~~~-~~~~~r~~gf~~~~~~~g 150 (265)
T cd06354 90 VVDDPPNVASIVFKEEEGSFLAGYLAALMT-KTGKVGFIGGMDI-PLIRRFEAGFEAGVKYVN 150 (265)
T ss_pred ccCCCCcEEEEEecchhHHHHHHHHHHhhc-CCCeEEEEecccC-hHHHHHHHHHHHHHHHHh
Confidence 22 1122222333211111112233333 5689999987643 222222345677777878
No 36
>cd06298 PBP1_CcpA_like Ligand-binding domain of the catabolite control protein A (CcpA), which functions as the major transcriptional regulator of carbon catabolite repression/regulation. Ligand-binding domain of the catabolite control protein A (CcpA), which functions as the major transcriptional regulator of carbon catabolite repression/regulation (CCR), a process in which enzymes necessary for the metabolism of alternative sugars are inhibited in the presence of glucose. In gram-positive bacteria, CCR is controlled by HPr, a phosphoenolpyruvate:sugar phsophotrasnferase system (PTS) and a transcriptional regulator CcpA. Moreover, CcpA can regulate sporulation and antibiotic resistance as well as play a role in virulence development of certain pathogens such as the group A streptococcus. The ligand binding domain of CcpA is a member of the LacI-GalR family of bacterial transcription regulators.
Probab=65.82 E-value=15 Score=32.69 Aligned_cols=60 Identities=10% Similarity=0.164 Sum_probs=39.2
Q ss_pred EEEEEEeCCCCCCcHHHHHHHHHHHHHcCCcEEEEEeCCCCHHH----HhcC-cCCccEEEEecCC
Q 042576 155 TWGIVLGTLGRQGNPRILERLQKRMEKKGFDYVVIMMSEISPAR----VALF-EDSVDAWIQIACP 215 (313)
Q Consensus 155 ~~GIIvgTLg~Q~~~~ii~~l~~ll~~~Gkk~y~i~v~einp~K----Lanf-~~~ID~fV~iaCP 215 (313)
+||+|+..+.-..+..+++.+++.+++.|....+.. +.-+++. +..+ ...+|++|++++.
T Consensus 1 ~i~vi~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~-~~~~~~~~~~~i~~l~~~~vdgiii~~~~ 65 (268)
T cd06298 1 TVGVIIPDITNSYFAELARGIDDIATMYKYNIILSN-SDNDKEKELKVLNNLLAKQVDGIIFMGGK 65 (268)
T ss_pred CEEEEECCCcchHHHHHHHHHHHHHHHcCCeEEEEe-CCCCHHHHHHHHHHHHHhcCCEEEEeCCC
Confidence 378888887777778888888888888887655443 3334432 2222 1148888887664
No 37
>cd06298 PBP1_CcpA_like Ligand-binding domain of the catabolite control protein A (CcpA), which functions as the major transcriptional regulator of carbon catabolite repression/regulation. Ligand-binding domain of the catabolite control protein A (CcpA), which functions as the major transcriptional regulator of carbon catabolite repression/regulation (CCR), a process in which enzymes necessary for the metabolism of alternative sugars are inhibited in the presence of glucose. In gram-positive bacteria, CCR is controlled by HPr, a phosphoenolpyruvate:sugar phsophotrasnferase system (PTS) and a transcriptional regulator CcpA. Moreover, CcpA can regulate sporulation and antibiotic resistance as well as play a role in virulence development of certain pathogens such as the group A streptococcus. The ligand binding domain of CcpA is a member of the LacI-GalR family of bacterial transcription regulators.
Probab=65.80 E-value=55 Score=29.00 Aligned_cols=130 Identities=10% Similarity=0.069 Sum_probs=66.2
Q ss_pred ccHhHHHHHHHHHHhCCCeEEecCCC--CCCCccccCCCCCCCCCCCCCCeEEEecCCcccHHHHHhhCCCceEEEeCCC
Q 042576 47 QFASAIRAAKPELEKQGFKVMIPQSK--PLSAGEVLGCTAPKIPARESDFNLVFIADGRFHLEAFMISNPGIKTFRYDPY 124 (313)
Q Consensus 47 Qf~~~l~~~~~~L~~~g~~v~ipq~~--pls~GevLGCt~~~~~~~~~~d~iv~igdGrFHle~~mi~np~~~~y~yDPy 124 (313)
.|...++.+.+.+++.|+.+++-... +-..-+++ ...+. ..+|++++.+.......--.+....+|++.+|-.
T Consensus 13 ~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~i---~~l~~--~~vdgiii~~~~~~~~~~~~l~~~~ipvV~~~~~ 87 (268)
T cd06298 13 YFAELARGIDDIATMYKYNIILSNSDNDKEKELKVL---NNLLA--KQVDGIIFMGGKISEEHREEFKRSPTPVVLAGSV 87 (268)
T ss_pred HHHHHHHHHHHHHHHcCCeEEEEeCCCCHHHHHHHH---HHHHH--hcCCEEEEeCCCCcHHHHHHHhcCCCCEEEEccc
Confidence 45555677888888888886652211 10000011 00011 2378888776432221112234457788877743
Q ss_pred C--CcccccccC---hHHHHHHHHHHHHHHhhcCCEEEEEEeCCC-CCCcHHHHHHHHHHHHHcCCcE
Q 042576 125 L--GKLFLEEYD---NKGMRETRKRAIEKAMKEARTWGIVLGTLG-RQGNPRILERLQKRMEKKGFDY 186 (313)
Q Consensus 125 s--~~~~~e~~d---~~~~l~~R~~~I~kak~~A~~~GIIvgTLg-~Q~~~~ii~~l~~ll~~~Gkk~ 186 (313)
. ..+.....| ..++..++ +++ + ..+++++|.|..+ ......-.+-.++.++++|.+.
T Consensus 88 ~~~~~~~~v~~d~~~~~~~~~~~--l~~--~-g~~~i~~l~~~~~~~~~~~~r~~gf~~~~~~~~~~~ 150 (268)
T cd06298 88 DEDNELPSVNIDYKKAAFEATEL--LIK--N-GHKKIAFISGPLEDSINGDERLAGYKEALSEANIEF 150 (268)
T ss_pred cCCCCCCEEEECcHHHHHHHHHH--HHH--c-CCceEEEEeCCcccccchhHHHHHHHHHHHHcCCCC
Confidence 1 112112222 22222222 222 4 6689999988766 4445555666778888888653
No 38
>PRK01045 ispH 4-hydroxy-3-methylbut-2-enyl diphosphate reductase; Reviewed
Probab=65.05 E-value=70 Score=31.03 Aligned_cols=119 Identities=18% Similarity=0.237 Sum_probs=73.5
Q ss_pred CCCeEEEEe-ccccHhHHHHHHHHHHhCCCeEEecCCCCCCCccccCCCCCCCCC------CCCCCeEEEecCCc----c
Q 042576 36 DPGKLILAG-TIQFASAIRAAKPELEKQGFKVMIPQSKPLSAGEVLGCTAPKIPA------RESDFNLVFIADGR----F 104 (313)
Q Consensus 36 ~~~~i~Lv~-tiQf~~~l~~~~~~L~~~g~~v~ipq~~pls~GevLGCt~~~~~~------~~~~d~iv~igdGr----F 104 (313)
..+++++++ |.|-....+.+.+.|+..++++.++..+ .| |.+..... ...+|++++||+-. -
T Consensus 154 ~~~~v~vvsQTT~~~~~~~~i~~~l~~~~~~~~v~~~n-----TI--C~aT~~RQ~a~~~La~~vD~miVVGg~~SsNT~ 226 (298)
T PRK01045 154 DPDKLALVTQTTLSVDDTAEIIAALKERFPEIQGPPKD-----DI--CYATQNRQEAVKELAPQADLVIVVGSKNSSNSN 226 (298)
T ss_pred CCCcEEEEEcCCCcHHHHHHHHHHHHHhCcCcccCCCC-----Cc--chhhHHHHHHHHHHHhhCCEEEEECCCCCccHH
Confidence 346788775 7788888999999999887776552211 12 65543210 02489999998743 2
Q ss_pred cHHHHHhhCCCceEEEeCCCCCcccccccChHHHHHHHHHHHHHHhhcCCEEEEEEeCCCCCCcHHHHHHHHHHHHHcC
Q 042576 105 HLEAFMISNPGIKTFRYDPYLGKLFLEEYDNKGMRETRKRAIEKAMKEARTWGIVLGTLGRQGNPRILERLQKRMEKKG 183 (313)
Q Consensus 105 Hle~~mi~np~~~~y~yDPys~~~~~e~~d~~~~l~~R~~~I~kak~~A~~~GIIvgTLg~Q~~~~ii~~l~~ll~~~G 183 (313)
||..+.-.. ..++|...-. ++.+. +..+ +.+++||.-|+ .---++++.+.+.|+..|
T Consensus 227 kL~~i~~~~-~~~t~~Ie~~------~el~~-----------~~l~-~~~~VGitaGA---STP~~li~eV~~~l~~~~ 283 (298)
T PRK01045 227 RLREVAEEA-GAPAYLIDDA------SEIDP-----------EWFK-GVKTVGVTAGA---SAPEWLVQEVIARLKELG 283 (298)
T ss_pred HHHHHHHHH-CCCEEEECCh------HHCcH-----------HHhc-CCCEEEEEecC---CCCHHHHHHHHHHHHHhC
Confidence 454444331 2456654422 12221 2336 78899999776 555668888888888764
No 39
>cd06279 PBP1_LacI_like_3 Ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. This group includes the ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.
Probab=64.94 E-value=14 Score=33.65 Aligned_cols=62 Identities=21% Similarity=0.338 Sum_probs=39.6
Q ss_pred EEEEEEeC-----CCCCCcHHHHHHHHHHHHHcCCcEEEEEeCCCCHHHHhcCc-CCccEEEEecCCCc
Q 042576 155 TWGIVLGT-----LGRQGNPRILERLQKRMEKKGFDYVVIMMSEISPARVALFE-DSVDAWIQIACPRL 217 (313)
Q Consensus 155 ~~GIIvgT-----Lg~Q~~~~ii~~l~~ll~~~Gkk~y~i~v~einp~KLanf~-~~ID~fV~iaCPrl 217 (313)
.||+|+-+ ..--....+++.+++.+++.|....++.... ..+.+.++. ..+|++|+.+++..
T Consensus 1 ~igvi~p~~~~~~~~~~~~~~~~~gi~~~a~~~g~~~~~~~~~~-~~~~~~~~~~~~~dgiii~~~~~~ 68 (283)
T cd06279 1 AVGVVLTDSLSYAFSDPVASQFLAGVAEVLDAAGVNLLLLPASS-EDSDSALVVSALVDGFIVYGVPRD 68 (283)
T ss_pred CEEEEeCCcccccccCccHHHHHHHHHHHHHHCCCEEEEecCcc-HHHHHHHHHhcCCCEEEEeCCCCC
Confidence 37888866 4555666788888888888887766654433 122233331 24888888888643
No 40
>cd06272 PBP1_hexuronate_repressor_like Ligand-binding domain of DNA transcription repressor for the hexuronate utilization operon from Bacillus species and its close homologs from other bacteria, all of which are a member of the LacI-GalR family of bacterial transcription regulators. Ligand-binding domain of DNA transcription repressor for the hexuronate utilization operon from Bacillus species and its close homologs from other bacteria, all of which are a member of the LacI-GalR family of bacterial transcription regulators. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor
Probab=64.74 E-value=15 Score=32.81 Aligned_cols=59 Identities=20% Similarity=0.364 Sum_probs=40.0
Q ss_pred EEEEEEeCCCCCCcHHHHHHHHHHHHHcCCcEEEEEeCCCCHHH-HhcCc-CCccEEEEecCC
Q 042576 155 TWGIVLGTLGRQGNPRILERLQKRMEKKGFDYVVIMMSEISPAR-VALFE-DSVDAWIQIACP 215 (313)
Q Consensus 155 ~~GIIvgTLg~Q~~~~ii~~l~~ll~~~Gkk~y~i~v~einp~K-Lanf~-~~ID~fV~iaCP 215 (313)
+||+|+.++....+..+++.+++.++++|....+.... +++. +..+. ..+|+.|+.+|.
T Consensus 1 ~igvv~~~~~~~~~~~~~~gi~~~~~~~g~~~~~~~~~--~~~~~~~~l~~~~vdgii~~~~~ 61 (261)
T cd06272 1 TIGLIWPSVSRVALTELVTGINQAISKNGYNMNVSITP--SLAEAEDLFKENRFDGVIIFGES 61 (261)
T ss_pred CEEEEecCCCchhHHHHHHHHHHHHHHcCCEEEEEecc--cHHHHHHHHHHcCcCEEEEeCCC
Confidence 47888888887788888889998888888776555443 2222 11221 148888887764
No 41
>cd06271 PBP1_AglR_RafR_like Ligand-binding domain of DNA transcription repressors specific for raffinose (RafR) and alpha-glucosides (AglR) which are members of the LacI-GalR family of bacterial transcription regulators. Ligand-binding domain of DNA transcription repressors specific for raffinose (RafR) and alpha-glucosides (AglR) which are members of the LacI-GalR family of bacterial transcription regulators. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the represso
Probab=64.60 E-value=21 Score=31.64 Aligned_cols=60 Identities=23% Similarity=0.295 Sum_probs=35.5
Q ss_pred EEEEEeC----CCCCCcHHHHHHHHHHHHHcCCcEEEEEeCCC-CHHH-HhcC--cCCccEEEEecCC
Q 042576 156 WGIVLGT----LGRQGNPRILERLQKRMEKKGFDYVVIMMSEI-SPAR-VALF--EDSVDAWIQIACP 215 (313)
Q Consensus 156 ~GIIvgT----Lg~Q~~~~ii~~l~~ll~~~Gkk~y~i~v~ei-np~K-Lanf--~~~ID~fV~iaCP 215 (313)
||||+.+ ..-..+..+++.+++.+++.|....++....- +..+ +..+ ...+|++|..+|.
T Consensus 2 igvi~p~~~~~~~~~~~~~~~~~i~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~vdgiii~~~~ 69 (268)
T cd06271 2 IGLVLPTGEREEGDPFFAEFLSGLSEALAEHGYDLVLLPVDPDEDPLEVYRRLVESGLVDGVIISRTR 69 (268)
T ss_pred eEEEeCCcccccCCccHHHHHHHHHHHHHHCCceEEEecCCCcHHHHHHHHHHHHcCCCCEEEEecCC
Confidence 6788766 33566677888888888888877655554422 1111 1111 1147888877663
No 42
>cd01542 PBP1_TreR_like Ligand-binding domain of DNA transcription repressor specific for trehalose (TreR) which is a member of the LacI-GalR family of bacterial transcription regulators. Ligand-binding domain of DNA transcription repressor specific for trehalose (TreR) which is a member of the LacI-GalR family of bacterial transcription regulators. The ligand-binding domain of TreR is structurally homologous to the periplasmic sugar-binding domain of ABC-type transporters and both domains contain the type I periplasmic binding protein-like fold. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the type I periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding wh
Probab=64.50 E-value=14 Score=32.85 Aligned_cols=60 Identities=17% Similarity=0.347 Sum_probs=38.2
Q ss_pred EEEEEEeCCCCCCcHHHHHHHHHHHHHcCCcEEEEEeCCCCHHHH----hcC-cCCccEEEEecCC
Q 042576 155 TWGIVLGTLGRQGNPRILERLQKRMEKKGFDYVVIMMSEISPARV----ALF-EDSVDAWIQIACP 215 (313)
Q Consensus 155 ~~GIIvgTLg~Q~~~~ii~~l~~ll~~~Gkk~y~i~v~einp~KL----anf-~~~ID~fV~iaCP 215 (313)
.||+|+..........+++.+++.+++.|.+..++. +.-++++. .++ ...+|++|.+++.
T Consensus 1 ~igvv~~~~~~~~~~~~~~gi~~~~~~~g~~~~~~~-~~~~~~~~~~~i~~l~~~~~dgii~~~~~ 65 (259)
T cd01542 1 LIGVIVPRLDSFSTSRTVKGILAALYENGYQMLLMN-TNFSIEKEIEALELLARQKVDGIILLATT 65 (259)
T ss_pred CeEEEecCCccchHHHHHHHHHHHHHHCCCEEEEEe-CCCCHHHHHHHHHHHHhcCCCEEEEeCCC
Confidence 378888777666667788888888888887754443 34445432 122 1148888887653
No 43
>cd06273 PBP1_GntR_like_1 This group includes the ligand-binding domain of putative DNA transcription repressors which are highly similar to that of the repressor specific for gluconate (GntR), a member of the LacI-GalR family of bacterial transcription regulators. This group includes the ligand-binding domain of putative DNA transcription repressors which are highly similar to that of the repressor specific for gluconate (GntR), a member of the LacI-GalR family of bacterial transcription regulators. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational
Probab=63.98 E-value=15 Score=32.67 Aligned_cols=77 Identities=21% Similarity=0.259 Sum_probs=46.0
Q ss_pred EEEEEEeCCCCCCcHHHHHHHHHHHHHcCCcEEEEEeCCCCHHHHh----cC-cCCccEEEEecCCCcc--ccccCCCCC
Q 042576 155 TWGIVLGTLGRQGNPRILERLQKRMEKKGFDYVVIMMSEISPARVA----LF-EDSVDAWIQIACPRLS--IDWGDAFTK 227 (313)
Q Consensus 155 ~~GIIvgTLg~Q~~~~ii~~l~~ll~~~Gkk~y~i~v~einp~KLa----nf-~~~ID~fV~iaCPrls--id~~~~f~k 227 (313)
++|+|+..+.-..+..+++.+.+.+++.|....++ -++-++++-. .+ ...+|++|++++.... +..-..-..
T Consensus 1 ~i~vv~p~~~~~~~~~~~~~i~~~~~~~g~~~~~~-~~~~~~~~~~~~~~~l~~~~vdgiii~~~~~~~~~~~~l~~~~i 79 (268)
T cd06273 1 TIGAIVPTLDNAIFARVIQAFQETLAAHGYTLLVA-SSGYDLDREYAQARKLLERGVDGLALIGLDHSPALLDLLARRGV 79 (268)
T ss_pred CeEEEeCCCCCchHHHHHHHHHHHHHHCCCEEEEe-cCCCCHHHHHHHHHHHHhcCCCEEEEeCCCCCHHHHHHHHhCCC
Confidence 47888888777778888888998898888555442 3344444221 11 1148888888764221 122223345
Q ss_pred cccCH
Q 042576 228 PLLTP 232 (313)
Q Consensus 228 PvLTP 232 (313)
|++..
T Consensus 80 Pvv~~ 84 (268)
T cd06273 80 PYVAT 84 (268)
T ss_pred CEEEE
Confidence 66554
No 44
>PRK10014 DNA-binding transcriptional repressor MalI; Provisional
Probab=63.94 E-value=23 Score=33.11 Aligned_cols=79 Identities=13% Similarity=0.169 Sum_probs=52.5
Q ss_pred cCCEEEEEEeCCCCCCcHHHHHHHHHHHHHcCCcEEEEEeCCCCHHHHh----cCc-CCccEEEEecCCCcc---ccccC
Q 042576 152 EARTWGIVLGTLGRQGNPRILERLQKRMEKKGFDYVVIMMSEISPARVA----LFE-DSVDAWIQIACPRLS---IDWGD 223 (313)
Q Consensus 152 ~A~~~GIIvgTLg~Q~~~~ii~~l~~ll~~~Gkk~y~i~v~einp~KLa----nf~-~~ID~fV~iaCPrls---id~~~ 223 (313)
..+++|+|+..+.-..+..+++.+.+.++++|...+++. +.-++++.. .+. ..+|++|+.+..... +++..
T Consensus 63 ~~~~Igvv~~~~~~~~~~~i~~gi~~~a~~~g~~~~~~~-~~~~~~~~~~~~~~l~~~~vdgiIi~~~~~~~~~~~~~l~ 141 (342)
T PRK10014 63 QSGVIGLIVRDLSAPFYAELTAGLTEALEAQGRMVFLLQ-GGKDGEQLAQRFSTLLNQGVDGVVIAGAAGSSDDLREMAE 141 (342)
T ss_pred CCCEEEEEeCCCccchHHHHHHHHHHHHHHcCCEEEEEe-CCCCHHHHHHHHHHHHhCCCCEEEEeCCCCCcHHHHHHHh
Confidence 557999999988878888899999999999997665543 333444322 221 149999998765321 22333
Q ss_pred CCCCcccC
Q 042576 224 AFTKPLLT 231 (313)
Q Consensus 224 ~f~kPvLT 231 (313)
....|+++
T Consensus 142 ~~~iPvV~ 149 (342)
T PRK10014 142 EKGIPVVF 149 (342)
T ss_pred hcCCCEEE
Confidence 44567764
No 45
>PRK15408 autoinducer 2-binding protein lsrB; Provisional
Probab=63.51 E-value=1.4e+02 Score=28.65 Aligned_cols=176 Identities=11% Similarity=0.125 Sum_probs=85.7
Q ss_pred CCCeEEEEec---cc-cHhHHHHHHHHHHhCCCeEEe-cCCCCCCCccccCCCCCCCCCCCCCCeEEEecCCcccHHHHH
Q 042576 36 DPGKLILAGT---IQ-FASAIRAAKPELEKQGFKVMI-PQSKPLSAGEVLGCTAPKIPARESDFNLVFIADGRFHLEAFM 110 (313)
Q Consensus 36 ~~~~i~Lv~t---iQ-f~~~l~~~~~~L~~~g~~v~i-pq~~pls~GevLGCt~~~~~~~~~~d~iv~igdGrFHle~~m 110 (313)
...+|+++.- .. |....+.+.+..++.|+++++ .....-...|+- .--..+. ..+|+|++.+-..-.+....
T Consensus 22 ~~~~i~~v~k~~~~pf~~~~~~Gi~~aa~~~G~~v~~~~~~~~d~~~q~~-~i~~li~--~~vdgIiv~~~d~~al~~~l 98 (336)
T PRK15408 22 AAERIAFIPKLVGVGFFTSGGNGAKEAGKELGVDVTYDGPTEPSVSGQVQ-LINNFVN--QGYNAIIVSAVSPDGLCPAL 98 (336)
T ss_pred CCcEEEEEECCCCCHHHHHHHHHHHHHHHHhCCEEEEECCCCCCHHHHHH-HHHHHHH--cCCCEEEEecCCHHHHHHHH
Confidence 3456776642 23 344456688888889998765 111110111110 0000011 24789888653211111111
Q ss_pred --hhCCCceEEEeCCCCC---cccccccChHHHHHHHH-HHHHHHhh-cCCEEEEEEeCCCCCCcHHHHHHHHHHHHHcC
Q 042576 111 --ISNPGIKTFRYDPYLG---KLFLEEYDNKGMRETRK-RAIEKAMK-EARTWGIVLGTLGRQGNPRILERLQKRMEKKG 183 (313)
Q Consensus 111 --i~np~~~~y~yDPys~---~~~~e~~d~~~~l~~R~-~~I~kak~-~A~~~GIIvgTLg~Q~~~~ii~~l~~ll~~~G 183 (313)
.....+|++.+|-... .......+......++. .++.+... ...+++|+.|+.+......-.+-.++.+++++
T Consensus 99 ~~a~~~gIpVV~~d~~~~~~~~~~~V~~~~~~~~G~~~~~~l~~~l~~g~gki~il~g~~~~~~~~~r~~g~~~~l~~~~ 178 (336)
T PRK15408 99 KRAMQRGVKVLTWDSDTKPECRSYYINQGTPEQLGSMLVEMAAKQVGKDKAKVAFFYSSPTVTDQNQWVKEAKAKIAKEH 178 (336)
T ss_pred HHHHHCCCeEEEeCCCCCCccceEEEecCCHHHHHHHHHHHHHHhcCCCCCEEEEEECCCCCccHHHHHHHHHHHHHhhC
Confidence 2235789999986532 11100111111222221 22333321 35789999998876655444566666665544
Q ss_pred CcEEEEE--eCCCCHH--------HHhcCcCCccEEEEecCC
Q 042576 184 FDYVVIM--MSEISPA--------RVALFEDSVDAWIQIACP 215 (313)
Q Consensus 184 kk~y~i~--v~einp~--------KLanf~~~ID~fV~iaCP 215 (313)
.+..++. -+.-+.+ -|...+ ++|+++-....
T Consensus 179 p~~~vv~~~~~~~d~~~a~~~~~~lL~~~p-di~aI~~~~~~ 219 (336)
T PRK15408 179 PGWEIVTTQFGYNDATKSLQTAEGILKAYP-DLDAIIAPDAN 219 (336)
T ss_pred CCCEEEeecCCCCcHHHHHHHHHHHHHHCC-CCcEEEECCCc
Confidence 4433332 2333333 356667 79998865443
No 46
>PRK05568 flavodoxin; Provisional
Probab=63.30 E-value=40 Score=27.77 Aligned_cols=56 Identities=14% Similarity=0.196 Sum_probs=42.2
Q ss_pred EEEEEEeCCCCCCcHHHHHHHHHHHHHcCCcEEEEEeCCCCHHHHhcCcCCccEEEEecCCC
Q 042576 155 TWGIVLGTLGRQGNPRILERLQKRMEKKGFDYVVIMMSEISPARVALFEDSVDAWIQIACPR 216 (313)
Q Consensus 155 ~~GIIvgTLg~Q~~~~ii~~l~~ll~~~Gkk~y~i~v~einp~KLanf~~~ID~fV~iaCPr 216 (313)
++.|+..|. --+...+++.|.+.+++.|.++.++-+.+....+|.+ .|. |++++|=
T Consensus 3 ~~~IvY~S~-~GnT~~~a~~i~~~~~~~g~~v~~~~~~~~~~~~~~~----~d~-iilgsp~ 58 (142)
T PRK05568 3 KINIIYWSG-TGNTEAMANLIAEGAKENGAEVKLLNVSEASVDDVKG----ADV-VALGSPA 58 (142)
T ss_pred eEEEEEECC-CchHHHHHHHHHHHHHHCCCeEEEEECCCCCHHHHHh----CCE-EEEECCc
Confidence 577888883 3455579999999999999998888888888776543 554 6667765
No 47
>cd06278 PBP1_LacI_like_2 Ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. This group includes the ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.
Probab=63.29 E-value=1.1e+02 Score=27.03 Aligned_cols=140 Identities=14% Similarity=0.109 Sum_probs=66.3
Q ss_pred ccHhHHHHHHHHHHhCCCeEEecCCCCC-CCccccCCCCCCCCCCCCCCeEEEecCCcccHHHHH-hhCCCceEEEeCCC
Q 042576 47 QFASAIRAAKPELEKQGFKVMIPQSKPL-SAGEVLGCTAPKIPARESDFNLVFIADGRFHLEAFM-ISNPGIKTFRYDPY 124 (313)
Q Consensus 47 Qf~~~l~~~~~~L~~~g~~v~ipq~~pl-s~GevLGCt~~~~~~~~~~d~iv~igdGrFHle~~m-i~np~~~~y~yDPy 124 (313)
.|...++.+.+.+++.|+.+.+-....- ...+.+ ...+. ..+|++++.+.. .....+. +..-++|++.+|-.
T Consensus 13 ~~~~~~~~i~~~~~~~g~~~~~~~~~~~~~~~~~i---~~~~~--~~vdgiii~~~~-~~~~~~~~~~~~~ipvV~~~~~ 86 (266)
T cd06278 13 FYSELLEALSRALQARGYQPLLINTDDDEDLDAAL---RQLLQ--YRVDGVIVTSGT-LSSELAEECRRNGIPVVLINRY 86 (266)
T ss_pred hHHHHHHHHHHHHHHCCCeEEEEcCCCCHHHHHHH---HHHHH--cCCCEEEEecCC-CCHHHHHHHhhcCCCEEEECCc
Confidence 3555566677777777777554211100 000110 00001 136777765432 1211111 22336788777743
Q ss_pred C--CcccccccChHHHHHHHHHHHHH--HhhcCCEEEEEEeCCCCCCcHHHHHHHHHHHHHcCCcEEEEEeCCCCH
Q 042576 125 L--GKLFLEEYDNKGMRETRKRAIEK--AMKEARTWGIVLGTLGRQGNPRILERLQKRMEKKGFDYVVIMMSEISP 196 (313)
Q Consensus 125 s--~~~~~e~~d~~~~l~~R~~~I~k--ak~~A~~~GIIvgTLg~Q~~~~ii~~l~~ll~~~Gkk~y~i~v~einp 196 (313)
. ..+.....|..++-+ . +.+. .+ ..+++++|.|..+.+....-.+-.++.++++|.+...+..+.-+.
T Consensus 87 ~~~~~~~~v~~d~~~~g~-~--~~~~l~~~-g~~~i~~i~~~~~~~~~~~R~~gf~~~~~~~~~~~~~~~~~~~~~ 158 (266)
T cd06278 87 VDGPGVDAVCSDNYEAGR-L--AAELLLAK-GCRRIAFIGGPADTSTSRERERGFRDALAAAGVPVVVEEAGDYSY 158 (266)
T ss_pred cCCCCCCEEEEChHHHHH-H--HHHHHHHC-CCceEEEEcCCCcccchHHHHHHHHHHHHHcCCChhhhccCCCCH
Confidence 2 122222334332221 1 1111 23 557899998876655444555667777888887643333444443
No 48
>cd06270 PBP1_GalS_like Ligand binding domain of DNA transcription iso-repressor GalS, which is one of two regulatory proteins involved in galactose transport and metabolism. Ligand binding domain of DNA transcription iso-repressor GalS, which is one of two regulatory proteins involved in galactose transport and metabolism. Transcription of the galactose regulon genes is regulated by Gal iso-repressor (GalS) and Gal repressor (GalR) in different ways, but both repressors recognize the same DNA binding site in the absence of D-galactose. GalS is a dimeric protein like GalR,and its major role is in regulating expression of the high-affinity galactose transporter encoded by the mgl operon, whereas GalR is the exclusive regulator of galactose permease, the low-affinity galactose transporter. GalS and GalR are members of the LacI-GalR family of transcription regulators and both contain the type I periplasmic binding protein-like fold. Hence, they are homologous to the periplasmic sugar bindi
Probab=63.21 E-value=26 Score=31.34 Aligned_cols=60 Identities=20% Similarity=0.256 Sum_probs=38.7
Q ss_pred EEEEEEeCCCCCCcHHHHHHHHHHHHHcCCcEEEEEeCCCCHHH----HhcC-cCCccEEEEecCC
Q 042576 155 TWGIVLGTLGRQGNPRILERLQKRMEKKGFDYVVIMMSEISPAR----VALF-EDSVDAWIQIACP 215 (313)
Q Consensus 155 ~~GIIvgTLg~Q~~~~ii~~l~~ll~~~Gkk~y~i~v~einp~K----Lanf-~~~ID~fV~iaCP 215 (313)
++|+|+..+.-..+..+++.+++.++++|....++. +.-++++ |.++ ...+|++|+.+|.
T Consensus 1 ~igvi~p~~~~~~~~~~~~g~~~~a~~~g~~~~~~~-~~~~~~~~~~~i~~~~~~~vdgii~~~~~ 65 (268)
T cd06270 1 TIGLVVSDLDGPFFGPLLSGVESVARKAGKHLIITA-GHHSAEKEREAIEFLLERRCDALILHSKA 65 (268)
T ss_pred CEEEEEccccCcchHHHHHHHHHHHHHCCCEEEEEe-CCCchHHHHHHHHHHHHcCCCEEEEecCC
Confidence 378888888777777888888888888887655433 3333332 1122 1248888887764
No 49
>PF04392 ABC_sub_bind: ABC transporter substrate binding protein; InterPro: IPR007487 ABC transporters belong to the ATP-Binding Cassette (ABC) superfamily, which uses the hydrolysis of ATP to energize diverse biological systems. ABC transporters are minimally constituted of two conserved regions: a highly conserved ATP binding cassette (ABC) and a less conserved transmembrane domain (TMD). These regions can be found on the same protein or on two different ones. Most ABC transporters function as a dimer and therefore are constituted of four domains, two ABC modules and two TMDs. This family contains many hypothetical proteins and some ABC transporter substrate binding proteins.; PDB: 3LFT_A 3LKV_A.
Probab=62.73 E-value=14 Score=34.78 Aligned_cols=103 Identities=17% Similarity=0.241 Sum_probs=64.8
Q ss_pred HHHHHHHHHHHHHhhcCCEEEEEEeCCCCCCcHHHHHHHHHHHHHcCCcEEEEEeCCCCH--HHHhcCcCCccEEEEecC
Q 042576 137 GMRETRKRAIEKAMKEARTWGIVLGTLGRQGNPRILERLQKRMEKKGFDYVVIMMSEISP--ARVALFEDSVDAWIQIAC 214 (313)
Q Consensus 137 ~~l~~R~~~I~kak~~A~~~GIIvgTLg~Q~~~~ii~~l~~ll~~~Gkk~y~i~v~einp--~KLanf~~~ID~fV~iaC 214 (313)
..+.++..++.+..-+++++|+|...-- ++....++.+++.+++.|.+.+.+.+...+. ..+..+.+.+|++++...
T Consensus 115 ~~~~~~l~l~~~l~P~~k~igvl~~~~~-~~~~~~~~~~~~~a~~~g~~l~~~~v~~~~~~~~~~~~l~~~~da~~~~~~ 193 (294)
T PF04392_consen 115 PPIEKQLELIKKLFPDAKRIGVLYDPSE-PNSVAQIEQLRKAAKKLGIELVEIPVPSSEDLEQALEALAEKVDALYLLPD 193 (294)
T ss_dssp --HHHHHHHHHHHSTT--EEEEEEETT--HHHHHHHHHHHHHHHHTT-EEEEEEESSGGGHHHHHHHHCTT-SEEEE-S-
T ss_pred cCHHHHHHHHHHhCCCCCEEEEEecCCC-ccHHHHHHHHHHHHHHcCCEEEEEecCcHhHHHHHHHHhhccCCEEEEECC
Confidence 3466777777777536899999997643 3456789999999999999999888887663 444455446898887754
Q ss_pred CCcc-----c-cccCCCCCcccCHHHHHHHhC
Q 042576 215 PRLS-----I-DWGDAFTKPLLTPFEAEIALG 240 (313)
Q Consensus 215 Prls-----i-d~~~~f~kPvLTPyE~~vAL~ 240 (313)
+-.. | ........|+++.++..|--|
T Consensus 194 ~~~~~~~~~i~~~~~~~~iPv~~~~~~~v~~G 225 (294)
T PF04392_consen 194 NLVDSNFEAILQLANEAKIPVFGSSDFYVKAG 225 (294)
T ss_dssp HHHHHTHHHHHHHCCCTT--EEESSHHHHCTT
T ss_pred cchHhHHHHHHHHHHhcCCCEEECCHHHhcCC
Confidence 4210 1 123467789998888777544
No 50
>cd06310 PBP1_ABC_sugar_binding_like_2 Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems. Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily, which consists of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis.
Probab=62.55 E-value=12 Score=33.69 Aligned_cols=62 Identities=10% Similarity=-0.069 Sum_probs=39.0
Q ss_pred EEEEEEeCCCCCCcHHHHHHHHHHHHHcCCcEEEEEeC-CCCHHHHh----cC-cCCccEEEEecCCC
Q 042576 155 TWGIVLGTLGRQGNPRILERLQKRMEKKGFDYVVIMMS-EISPARVA----LF-EDSVDAWIQIACPR 216 (313)
Q Consensus 155 ~~GIIvgTLg~Q~~~~ii~~l~~ll~~~Gkk~y~i~v~-einp~KLa----nf-~~~ID~fV~iaCPr 216 (313)
+||+|+.++.-.....+++.+++.++++|....++... .=++++.. ++ ...+|+.|..++..
T Consensus 1 ~Igvi~~~~~~~~~~~~~~g~~~~~~~~g~~~~~~~~~~~~~~~~~~~~i~~l~~~~vdgvii~~~~~ 68 (273)
T cd06310 1 KIALVPKGTTSDFWQAVKAGAEAAAKELGVKVTFQGPASETDVAGQVNLLENAIARGPDAILLAPTDA 68 (273)
T ss_pred CeEEEecCCCcHHHHHHHHHHHHHHHHcCCEEEEecCccCCCHHHHHHHHHHHHHhCCCEEEEcCCCh
Confidence 47888888777777788888888888888665544321 22444322 11 11488888766644
No 51
>cd01545 PBP1_SalR Ligand-binding domain of DNA transcription repressor SalR, a member of the LacI-GalR family of bacterial transcription regulators. Ligand-binding domain of DNA transcription repressor SalR, a member of the LacI-GalR family of bacterial transcription regulators. The SalR binds to glucose based compound Salicin which is chemically related to aspirin. The ligand-binding of SalR is structurally homologous to the periplasmic sugar-binding domain of ABC-transporters and both domains contain the type I periplasmic binding protein-like fold. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the type I periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand bind
Probab=62.49 E-value=32 Score=30.60 Aligned_cols=60 Identities=20% Similarity=0.189 Sum_probs=36.7
Q ss_pred EEEEEEeCCCCCCcHHHHHHHHHHHHHcCCcEEEEEeCCCCH---HHHh-cC-cCCccEEEEecC
Q 042576 155 TWGIVLGTLGRQGNPRILERLQKRMEKKGFDYVVIMMSEISP---ARVA-LF-EDSVDAWIQIAC 214 (313)
Q Consensus 155 ~~GIIvgTLg~Q~~~~ii~~l~~ll~~~Gkk~y~i~v~einp---~KLa-nf-~~~ID~fV~iaC 214 (313)
.||+|+....-.....+++-+++.+++.|....++..++-.+ ..+. .+ ...+|++|+..+
T Consensus 1 ~I~vi~~~~~~~~~~~~~~gi~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~l~~~~vdgiii~~~ 65 (270)
T cd01545 1 LIGLLYDNPSPGYVSEIQLGALDACRDTGYQLVIEPCDSGSPDLAERVRALLQRSRVDGVILTPP 65 (270)
T ss_pred CEEEEEcCCCcccHHHHHHHHHHHHHhCCCeEEEEeCCCCchHHHHHHHHHHHHCCCCEEEEeCC
Confidence 367777777667777777888888887777766655553322 1111 11 114777777765
No 52
>COG1609 PurR Transcriptional regulators [Transcription]
Probab=62.47 E-value=42 Score=32.31 Aligned_cols=61 Identities=16% Similarity=0.343 Sum_probs=51.1
Q ss_pred cCCEEEEEEeCCCCCCcHHHHHHHHHHHHHcCCcEEEEEeCCCCHHHHhcC----c-CCccEEEEec
Q 042576 152 EARTWGIVLGTLGRQGNPRILERLQKRMEKKGFDYVVIMMSEISPARVALF----E-DSVDAWIQIA 213 (313)
Q Consensus 152 ~A~~~GIIvgTLg~Q~~~~ii~~l~~ll~~~Gkk~y~i~v~einp~KLanf----~-~~ID~fV~ia 213 (313)
..+.+|+|+..+....+.++++.|++.++++|+...+...++ ++++.... . ..+|.+|+.+
T Consensus 57 ~s~~Ig~i~p~~~~~~~~~i~~gi~~~~~~~gy~~~l~~~~~-~~~~e~~~~~~l~~~~vdGiIi~~ 122 (333)
T COG1609 57 RTKTIGLVVPDITNPFFAEILKGIEEAAREAGYSLLLANTDD-DPEKEREYLETLLQKRVDGLILLG 122 (333)
T ss_pred CCCEEEEEeCCCCCchHHHHHHHHHHHHHHcCCEEEEECCCC-CHHHHHHHHHHHHHcCCCEEEEec
Confidence 578999999999999999999999999999999988888777 77763322 1 2499999998
No 53
>PF00885 DMRL_synthase: 6,7-dimethyl-8-ribityllumazine synthase; InterPro: IPR002180 6,7-dimethyl-8-ribityllumazine synthase (riboflavin synthase) catalyses the biosynthesis of riboflavin according to the reaction: 2 6,7-dimethyl-8-(1-D-ribityl)lumazine = riboflavin + 4-(1-D-ribitylamino)-5-amino-2,6-dihydroxypyrimidine. The biosynthesis of one riboflavin molecule requires one molecule of GTP and two molecules of ribulose 5-phosphate as substrates. The final step in the biosynthesis of the vitamin involves the dismutation of 6,7-dimethyl-8-ribityllumazine catalyzed by riboflavin synthase. The second product, 5-amino-6-ribitylamino-2,4(1H,3H)-pyrimidinedione, is recycled in the biosynthetic pathway by 6,7-dimethyl-8-ribityllumazine synthase []. N-[2,4-dioxo-6-d-ribitylamino-1,2,3,4-tetrahydropyrimidin-5-yl]oxalamic acid derivatives inhibit riboflavin synthase []. This family includes the beta chain of 6,7-dimethyl-8-ribityllumazine synthase 2.5.1.9 from EC. The family also includes a subfamily of distant archaebacterial proteins that may also have the same function for example O28856 from SWISSPROT.; GO: 0009231 riboflavin biosynthetic process, 0009349 riboflavin synthase complex; PDB: 2O6H_D 1C41_C 2OBX_H 1VSX_H 1VSW_3 3JV8_C 3MK3_r 3NQ4_G 2A58_A 2A57_D ....
Probab=62.13 E-value=24 Score=30.50 Aligned_cols=87 Identities=26% Similarity=0.330 Sum_probs=58.0
Q ss_pred CCEEEEEEeCCCCCCcHHHHHHHHHHHHHcCC---cEEEEEeCCCC-----HHHHhcCcCCccEEEEecC-CCcccc---
Q 042576 153 ARTWGIVLGTLGRQGNPRILERLQKRMEKKGF---DYVVIMMSEIS-----PARVALFEDSVDAWIQIAC-PRLSID--- 220 (313)
Q Consensus 153 A~~~GIIvgTLg~Q~~~~ii~~l~~ll~~~Gk---k~y~i~v~ein-----p~KLanf~~~ID~fV~iaC-Prlsid--- 220 (313)
.-+||||.+.--..-.-.+++...+.|++.|. ...++.|--.. ..+|.... .+|++|.++| =|...+
T Consensus 3 ~~ri~IV~s~~n~~i~~~ll~~a~~~l~~~g~~~~~i~~~~VPGa~ElP~a~~~l~~~~-~~Davi~lG~VI~G~T~H~~ 81 (144)
T PF00885_consen 3 GLRIAIVVSRFNEEITDRLLEGALEELKRHGVAEENIEVIRVPGAFELPLAAKRLAESG-RYDAVIALGCVIRGETDHFE 81 (144)
T ss_dssp TEEEEEEEESTTHHHHHHHHHHHHHHHHHTTTTGGCEEEEEESSGGGHHHHHHHHHHCS-TESEEEEEEEEE--SSTHHH
T ss_pred CCEEEEEEEeccHHHHHHHHHHHHHHHHHcCCCccceEEEEcCCHHHHHHHHHHHhccc-CccEEEEeccccCCCchHHH
Confidence 34799999876555455555556788889987 77888877654 46777777 7999999998 332221
Q ss_pred ------------ccCCCCCc----ccCHHHHHHHhC
Q 042576 221 ------------WGDAFTKP----LLTPFEAEIALG 240 (313)
Q Consensus 221 ------------~~~~f~kP----vLTPyE~~vAL~ 240 (313)
=+-++.+| ||||-+.+-|+.
T Consensus 82 ~v~~~v~~gl~~lsl~~~~PV~~gvlt~~~~eqa~~ 117 (144)
T PF00885_consen 82 YVANAVSRGLMDLSLEYGIPVIFGVLTPDTEEQALE 117 (144)
T ss_dssp HHHHHHHHHHHHHHHHHTSEEEEEEEEESSHHHHHH
T ss_pred HHHHHHHHHHHHHhccCCccEEEEecCCCCHHHHHH
Confidence 12346677 466666666663
No 54
>PRK12360 4-hydroxy-3-methylbut-2-enyl diphosphate reductase; Provisional
Probab=62.03 E-value=70 Score=30.74 Aligned_cols=114 Identities=17% Similarity=0.195 Sum_probs=70.5
Q ss_pred CCeEEEEe-ccccHhHHHHHHHHHHhCCCeEEecCCCCCCCccccCCCCCCCCC------CCCCCeEEEecCCc----cc
Q 042576 37 PGKLILAG-TIQFASAIRAAKPELEKQGFKVMIPQSKPLSAGEVLGCTAPKIPA------RESDFNLVFIADGR----FH 105 (313)
Q Consensus 37 ~~~i~Lv~-tiQf~~~l~~~~~~L~~~g~~v~ipq~~pls~GevLGCt~~~~~~------~~~~d~iv~igdGr----FH 105 (313)
.+++++++ |.|-....+.+.+.|+.+++++.+. ..| |.+..... ...+|++++||+-. -|
T Consensus 156 ~~kv~~vsQTT~~~~~~~~iv~~l~~~~~~~~v~-------~TI--C~aT~~RQ~a~~~La~~vD~miVVGg~~SsNT~r 226 (281)
T PRK12360 156 LDKACVVAQTTIIPELWEDILNVIKLKSKELVFF-------NTI--CSATKKRQESAKELSKEVDVMIVIGGKHSSNTQK 226 (281)
T ss_pred ccCEEEEECCCCcHHHHHHHHHHHHHhCcccccC-------CCc--chhhhhHHHHHHHHHHhCCEEEEecCCCCccHHH
Confidence 36788775 7788889999999999888776542 223 44432110 02489999998743 24
Q ss_pred HHHHHhhCCCceEEEeCCCCCcccccccChHHHHHHHHHHHHHHhhcCCEEEEEEeCCCCCCcHHHHHHHHHHHHH
Q 042576 106 LEAFMISNPGIKTFRYDPYLGKLFLEEYDNKGMRETRKRAIEKAMKEARTWGIVLGTLGRQGNPRILERLQKRMEK 181 (313)
Q Consensus 106 le~~mi~np~~~~y~yDPys~~~~~e~~d~~~~l~~R~~~I~kak~~A~~~GIIvgTLg~Q~~~~ii~~l~~ll~~ 181 (313)
|..+.-.. ..++|..+-. ++.+. +..+ +.+++||.-|+ .---++++.+.+.|++
T Consensus 227 L~eia~~~-~~~t~~Ie~~------~el~~-----------~~~~-~~~~VGitaGA---STP~~li~eV~~~l~~ 280 (281)
T PRK12360 227 LVKICEKN-CPNTFHIETA------DELDL-----------EMLK-DYKIIGITAGA---STPDWIIEEVIKKIKN 280 (281)
T ss_pred HHHHHHHH-CCCEEEECCh------HHCCH-----------HHhC-CCCEEEEEccC---CCCHHHHHHHHHHHHh
Confidence 55555432 3356655432 12222 2445 78899998776 4445677777777653
No 55
>cd01542 PBP1_TreR_like Ligand-binding domain of DNA transcription repressor specific for trehalose (TreR) which is a member of the LacI-GalR family of bacterial transcription regulators. Ligand-binding domain of DNA transcription repressor specific for trehalose (TreR) which is a member of the LacI-GalR family of bacterial transcription regulators. The ligand-binding domain of TreR is structurally homologous to the periplasmic sugar-binding domain of ABC-type transporters and both domains contain the type I periplasmic binding protein-like fold. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the type I periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding wh
Probab=61.43 E-value=94 Score=27.39 Aligned_cols=129 Identities=9% Similarity=0.032 Sum_probs=61.2
Q ss_pred ccHhHHHHHHHHHHhCCCeEEecCCC--CCCCccccCCCCCCCCCCCCCCeEEEecCCcccHHH-HHhhCCCceEEEeCC
Q 042576 47 QFASAIRAAKPELEKQGFKVMIPQSK--PLSAGEVLGCTAPKIPARESDFNLVFIADGRFHLEA-FMISNPGIKTFRYDP 123 (313)
Q Consensus 47 Qf~~~l~~~~~~L~~~g~~v~ipq~~--pls~GevLGCt~~~~~~~~~~d~iv~igdGrFHle~-~mi~np~~~~y~yDP 123 (313)
.|...++.+.+.+++.|+++++-... +...-+.+.= .+. ..+|++++.+... .... -.+..-.+|++.+|-
T Consensus 13 ~~~~~~~gi~~~~~~~g~~~~~~~~~~~~~~~~~~i~~---l~~--~~~dgii~~~~~~-~~~~~~~~~~~~ipvv~~~~ 86 (259)
T cd01542 13 STSRTVKGILAALYENGYQMLLMNTNFSIEKEIEALEL---LAR--QKVDGIILLATTI-TDEHREAIKKLNVPVVVVGQ 86 (259)
T ss_pred hHHHHHHHHHHHHHHCCCEEEEEeCCCCHHHHHHHHHH---HHh--cCCCEEEEeCCCC-CHHHHHHHhcCCCCEEEEec
Confidence 44566777888888888887652211 1000001100 001 2378888775432 1111 122333578877774
Q ss_pred CCCcccccccChHHHHHHH-HHHHHHHhhcCCEEEEEEeCCCC-CCcHHHHHHHHHHHHHcCC
Q 042576 124 YLGKLFLEEYDNKGMRETR-KRAIEKAMKEARTWGIVLGTLGR-QGNPRILERLQKRMEKKGF 184 (313)
Q Consensus 124 ys~~~~~e~~d~~~~l~~R-~~~I~kak~~A~~~GIIvgTLg~-Q~~~~ii~~l~~ll~~~Gk 184 (313)
....+.....|....-+.- ..+++ + .-+++|++.+.... .....-.+-.++.++++|.
T Consensus 87 ~~~~~~~v~~d~~~~~~~~~~~l~~--~-g~~~i~~v~~~~~~~~~~~~r~~gf~~~~~~~~~ 146 (259)
T cd01542 87 DYPGISSVVYDDYGAGYELGEYLAQ--Q-GHKNIAYLGVSESDIAVGILRKQGYLDALKEHGI 146 (259)
T ss_pred cCCCCCEEEECcHHHHHHHHHHHHH--c-CCCcEEEEcCCcccchhHHHHHHHHHHHHHHcCC
Confidence 3222222223333322111 11222 4 56789888544221 1123445667777888886
No 56
>PRK11303 DNA-binding transcriptional regulator FruR; Provisional
Probab=60.56 E-value=40 Score=31.35 Aligned_cols=63 Identities=19% Similarity=0.373 Sum_probs=45.0
Q ss_pred cCCEEEEEEeCCCCCCcHHHHHHHHHHHHHcCCcEEEEEeCCCCHHHH----hcC-cCCccEEEEecCC
Q 042576 152 EARTWGIVLGTLGRQGNPRILERLQKRMEKKGFDYVVIMMSEISPARV----ALF-EDSVDAWIQIACP 215 (313)
Q Consensus 152 ~A~~~GIIvgTLg~Q~~~~ii~~l~~ll~~~Gkk~y~i~v~einp~KL----anf-~~~ID~fV~iaCP 215 (313)
..+++|+|+..+.-.....+++.+++.++++|....++... -++++. ..+ ...+|+.|+.++.
T Consensus 60 ~~~~Igvv~~~~~~~~~~~l~~gi~~~~~~~g~~~~~~~~~-~~~~~~~~~~~~l~~~~vdgiIi~~~~ 127 (328)
T PRK11303 60 RTRSIGLIIPDLENTSYARIAKYLERQARQRGYQLLIACSD-DQPDNEMRCAEHLLQRQVDALIVSTSL 127 (328)
T ss_pred CCceEEEEeCCCCCchHHHHHHHHHHHHHHcCCEEEEEeCC-CCHHHHHHHHHHHHHcCCCEEEEcCCC
Confidence 46789999988877788889999999999999887655433 234332 222 1249999987763
No 57
>cd06295 PBP1_CelR Ligand binding domain of a transcription regulator of cellulose genes, CelR, which is highly homologous to the LacI-GalR family of bacterial transcription regulators. This group includes the ligand binding domain of a transcription regulator of cellulose genes, CelR, which is highly homologous to the LacI-GalR family of bacterial transcription regulators. The binding of CelR to the celE promoter is inhibited specifically by cellobiose. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn chang
Probab=58.96 E-value=35 Score=30.63 Aligned_cols=64 Identities=16% Similarity=0.240 Sum_probs=42.1
Q ss_pred cCCEEEEEEeC-------CCCCCcHHHHHHHHHHHHHcCCcEEEEEeCCCCHHHHhcC--cCCccEEEEecCC
Q 042576 152 EARTWGIVLGT-------LGRQGNPRILERLQKRMEKKGFDYVVIMMSEISPARVALF--EDSVDAWIQIACP 215 (313)
Q Consensus 152 ~A~~~GIIvgT-------Lg~Q~~~~ii~~l~~ll~~~Gkk~y~i~v~einp~KLanf--~~~ID~fV~iaCP 215 (313)
..+++|||+.. +.-..+..+++.+++.+++.|.+..++..+.-...++..+ ...+|++|..+|.
T Consensus 2 ~s~~i~vi~p~~~~~~~~~~~~~~~~~~~gi~~~~~~~g~~~~v~~~~~~~~~~~~~~l~~~~~dgiii~~~~ 74 (275)
T cd06295 2 RTDTIALVVPEPHERDQSFSDPFFLSLLGGIADALAERGYDLLLSFVSSPDRDWLARYLASGRADGVILIGQH 74 (275)
T ss_pred CceEEEEEecCccccccccCCchHHHHHHHHHHHHHHcCCEEEEEeCCchhHHHHHHHHHhCCCCEEEEeCCC
Confidence 45788999854 4444567788889999998888877665543322233221 1258999888775
No 58
>COG2984 ABC-type uncharacterized transport system, periplasmic component [General function prediction only]
Probab=58.72 E-value=39 Score=33.14 Aligned_cols=196 Identities=17% Similarity=0.207 Sum_probs=109.1
Q ss_pred CCeEEEEeccccHhH---HHHHHHHHHhCCC-eEEe-cCCCCCCCccccCCCCCCCCCCCCCCeEEEecCCcccHHHHHh
Q 042576 37 PGKLILAGTIQFASA---IRAAKPELEKQGF-KVMI-PQSKPLSAGEVLGCTAPKIPARESDFNLVFIADGRFHLEAFMI 111 (313)
Q Consensus 37 ~~~i~Lv~tiQf~~~---l~~~~~~L~~~g~-~v~i-pq~~pls~GevLGCt~~~~~~~~~~d~iv~igdGrFHle~~mi 111 (313)
..+|++..-++|-.. .+.+++.|++.|+ ++.+ -+...-++|-..-= +..+.. +..|.++-++. --.-.++=
T Consensus 30 ~~~VaI~~~veHpaLd~~~~G~~~aLk~~G~~n~~i~~~na~~~~~~a~~i-arql~~-~~~dviv~i~t--p~Aq~~~s 105 (322)
T COG2984 30 QITVAITQFVEHPALDAAREGVKEALKDAGYKNVKIDYQNAQGDLGTAAQI-ARQLVG-DKPDVIVAIAT--PAAQALVS 105 (322)
T ss_pred ceeEEEEEeecchhHHHHHHHHHHHHHhcCccCeEEEeecCCCChHHHHHH-HHHhhc-CCCcEEEecCC--HHHHHHHH
Confidence 335777776666543 4556788888888 4333 11111011000000 000111 12344444433 22233333
Q ss_pred hCCCceEE---EeCCCCCccccc------c----cChHHHHHHHHHHHHHHhhcCCEEEEEEeCCCCCCcHHHHHHHHHH
Q 042576 112 SNPGIKTF---RYDPYLGKLFLE------E----YDNKGMRETRKRAIEKAMKEARTWGIVLGTLGRQGNPRILERLQKR 178 (313)
Q Consensus 112 ~np~~~~y---~yDPys~~~~~e------~----~d~~~~l~~R~~~I~kak~~A~~~GIIvgTLg~Q~~~~ii~~l~~l 178 (313)
+.-++|+. .=||.+.++... . -|.. -+.++-++|.+.-=++|++|++-+. |-++...+++.|++.
T Consensus 106 ~~~~iPVV~aavtd~v~a~Lv~~~~~pg~NvTGvsD~~-~v~q~i~lik~~~Pnak~Igv~Y~p-~E~ns~~l~eelk~~ 183 (322)
T COG2984 106 ATKTIPVVFAAVTDPVGAKLVKSLEQPGGNVTGVSDLL-PVAQQIELIKALLPNAKSIGVLYNP-GEANSVSLVEELKKE 183 (322)
T ss_pred hcCCCCEEEEccCchhhccCCccccCCCCceeecCCcc-hHHHHHHHHHHhCCCCeeEEEEeCC-CCcccHHHHHHHHHH
Confidence 33334532 345666655531 0 1221 2566777777665589999999987 457889999999999
Q ss_pred HHHcCCcEEEEEeCCCCHH--HHhcCcCCccEEEEecCCCccc-------cccCCCCCcccCHHHHHHHh
Q 042576 179 MEKKGFDYVVIMMSEISPA--RVALFEDSVDAWIQIACPRLSI-------DWGDAFTKPLLTPFEAEIAL 239 (313)
Q Consensus 179 l~~~Gkk~y~i~v~einp~--KLanf~~~ID~fV~iaCPrlsi-------d~~~~f~kPvLTPyE~~vAL 239 (313)
++++|.+.+...+...|.- -..+..+.+|++... |--+.. --......||+++-+-.|-=
T Consensus 184 A~~~Gl~vve~~v~~~ndi~~a~~~l~g~~d~i~~p-~dn~i~s~~~~l~~~a~~~kiPli~sd~~~V~~ 252 (322)
T COG2984 184 ARKAGLEVVEAAVTSVNDIPRAVQALLGKVDVIYIP-TDNLIVSAIESLLQVANKAKIPLIASDTSSVKE 252 (322)
T ss_pred HHHCCCEEEEEecCcccccHHHHHHhcCCCcEEEEe-cchHHHHHHHHHHHHHHHhCCCeecCCHHHHhc
Confidence 9999999999999776632 333443368876532 222211 12235678888888777653
No 59
>cd06283 PBP1_RegR_EndR_KdgR_like Ligand-binding domain of DNA transcription repressor RegR and other putative regulators such as KdgR and EndR. Ligand-binding domain of DNA transcription repressor RegR and other putative regulators such as KdgR and EndR, all of which are members of the LacI-GalR family of bacterial transcription regulators. RegR regulates bacterial competence and the expression of virulence factors, including hyaluronidase. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA b
Probab=58.64 E-value=29 Score=30.71 Aligned_cols=59 Identities=15% Similarity=0.248 Sum_probs=35.6
Q ss_pred EEEEEEeCCCCCCcHHHHHHHHHHHHHcCCcEEEEEeCCCCHHHHh----cCc-CCccEEEEecC
Q 042576 155 TWGIVLGTLGRQGNPRILERLQKRMEKKGFDYVVIMMSEISPARVA----LFE-DSVDAWIQIAC 214 (313)
Q Consensus 155 ~~GIIvgTLg~Q~~~~ii~~l~~ll~~~Gkk~y~i~v~einp~KLa----nf~-~~ID~fV~iaC 214 (313)
+||+|+....-.....+++.+++.+++.|....+.. ++-+++... .+- ..+|++|+.++
T Consensus 1 ~igvi~~~~~~~~~~~~~~~i~~~a~~~g~~~~~~~-~~~~~~~~~~~~~~l~~~~~dgiii~~~ 64 (267)
T cd06283 1 LIGVIVADITNPFSSLVLKGIEDVCRAHGYQVLVCN-SDNDPEKEKEYLESLLAYQVDGLIVNPT 64 (267)
T ss_pred CEEEEecCCccccHHHHHHHHHHHHHHcCCEEEEEc-CCCCHHHHHHHHHHHHHcCcCEEEEeCC
Confidence 367777777667777788888888887776654333 333443321 111 13777777665
No 60
>PRK14987 gluconate operon transcriptional regulator; Provisional
Probab=58.20 E-value=31 Score=32.24 Aligned_cols=63 Identities=16% Similarity=0.269 Sum_probs=44.8
Q ss_pred cCCEEEEEEeCCCCCCcHHHHHHHHHHHHHcCCcEEEEEeCCCCHHH----HhcCc-CCccEEEEecCC
Q 042576 152 EARTWGIVLGTLGRQGNPRILERLQKRMEKKGFDYVVIMMSEISPAR----VALFE-DSVDAWIQIACP 215 (313)
Q Consensus 152 ~A~~~GIIvgTLg~Q~~~~ii~~l~~ll~~~Gkk~y~i~v~einp~K----Lanf~-~~ID~fV~iaCP 215 (313)
..+.||+|+..+....+..+++.+++.++++|.+..+...+ -++++ +.++. ..+|.+|+.++.
T Consensus 62 ~~~~Igvi~~~~~~~~~~~~~~gi~~~~~~~g~~~~~~~~~-~~~~~~~~~~~~~~~~~vdgiI~~~~~ 129 (331)
T PRK14987 62 TSRAIGVLLPSLTNQVFAEVLRGIESVTDAHGYQTMLAHYG-YKPEMEQERLESMLSWNIDGLILTERT 129 (331)
T ss_pred CCCEEEEEeCCCcchhHHHHHHHHHHHHHHCCCEEEEecCC-CCHHHHHHHHHHHHhcCCCEEEEcCCC
Confidence 56799999998887788899999999999999776544332 23322 22331 259999987653
No 61
>cd01574 PBP1_LacI Ligand-binding domain of DNA transcription repressor LacI specific for lactose, a member of the LacI-GalR family of bacterial transcription regulators. Ligand-binding domain of DNA transcription repressor LacI specific for lactose, a member of the LacI-GalR family of bacterial transcription regulators. The ligand-binding domain of LacI is structurally homologous to the periplasmic sugar-binding domain of ABC-type transporters and both domains contain the type I periplasmic binding protein-like fold. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the type I periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA b
Probab=58.04 E-value=32 Score=30.54 Aligned_cols=61 Identities=23% Similarity=0.301 Sum_probs=38.5
Q ss_pred EEEEEEeCCCCCCcHHHHHHHHHHHHHcCCcEEEEEeCCCCHHH----HhcC-cCCccEEEEecCC
Q 042576 155 TWGIVLGTLGRQGNPRILERLQKRMEKKGFDYVVIMMSEISPAR----VALF-EDSVDAWIQIACP 215 (313)
Q Consensus 155 ~~GIIvgTLg~Q~~~~ii~~l~~ll~~~Gkk~y~i~v~einp~K----Lanf-~~~ID~fV~iaCP 215 (313)
+||+|+.+..-.....+++.+++.+++.|....++..+.-.+++ +..+ ...+|+.+..++-
T Consensus 1 ~i~vi~~~~~~~~~~~~~~gi~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~vdgiii~~~~ 66 (264)
T cd01574 1 TIGVVTTDLALHGPSSTLAAIESAAREAGYAVTLSMLAEADEEALRAAVRRLLAQRVDGVIVNAPL 66 (264)
T ss_pred CEEEEeCCCCcccHHHHHHHHHHHHHHCCCeEEEEeCCCCchHHHHHHHHHHHhcCCCEEEEeCCC
Confidence 37888877666667778888888888888776555544333221 1122 1148888877763
No 62
>cd06309 PBP1_YtfQ_like Periplasmic binding domain of ABC-type YtfQ-like transport systems. Periplasmic binding domain of ABC-type YtfQ-like transport systems. The YtfQ protein from Escherichia coli is up-regulated under glucose-limited conditions and shares homology with a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily. Members of this group are predicted to be involved in the transport of sugar-containing molecules across cellular and organellar membranes; however their ligand specificity is not determined experimentally.
Probab=57.70 E-value=1.4e+02 Score=26.66 Aligned_cols=134 Identities=10% Similarity=0.023 Sum_probs=65.7
Q ss_pred ccccHhHHHHHHHHHHhCCCeEEecCCCCCCCccccCCCCCCCCCCCCCCeEEEecCCccc--HHHH-HhhCCCceEEEe
Q 042576 45 TIQFASAIRAAKPELEKQGFKVMIPQSKPLSAGEVLGCTAPKIPARESDFNLVFIADGRFH--LEAF-MISNPGIKTFRY 121 (313)
Q Consensus 45 tiQf~~~l~~~~~~L~~~g~~v~ipq~~pls~GevLGCt~~~~~~~~~~d~iv~igdGrFH--le~~-mi~np~~~~y~y 121 (313)
+.-|...++.+.+.+++.|+++++-.... +..+-..+-...+. ..+|++++.+.. .. ...+ .+..-.+|++.+
T Consensus 11 ~~~~~~~~~~~~~~a~~~g~~~~~~~~~~-~~~~~~~~i~~l~~--~~vdgiIi~~~~-~~~~~~~i~~~~~~~iPvV~~ 86 (273)
T cd06309 11 SPWRTAETKSIKDAAEKRGFDLKFADAQQ-KQENQISAIRSFIA--QGVDVIILAPVV-ETGWDPVLKEAKAAGIPVILV 86 (273)
T ss_pred CHHHHHHHHHHHHHHHhcCCEEEEeCCCC-CHHHHHHHHHHHHH--cCCCEEEEcCCc-cccchHHHHHHHHCCCCEEEE
Confidence 33456667788888888899877622110 00000000000001 237888776532 12 1111 233346788888
Q ss_pred CCCCC------cccccccChHHHHHHH-HHHHHHHhhcCCEEEEEEeCCCCCCcHHHHHHHHHHHHHcC
Q 042576 122 DPYLG------KLFLEEYDNKGMRETR-KRAIEKAMKEARTWGIVLGTLGRQGNPRILERLQKRMEKKG 183 (313)
Q Consensus 122 DPys~------~~~~e~~d~~~~l~~R-~~~I~kak~~A~~~GIIvgTLg~Q~~~~ii~~l~~ll~~~G 183 (313)
|.... .+.....|....-+.= ..+++++. ..+++++|-|..+......-.+-+++-|++++
T Consensus 87 ~~~~~~~~~~~~~~~v~~d~~~~g~~~~~~l~~~~~-g~~~i~~i~~~~~~~~~~~R~~Gf~~~l~~~~ 154 (273)
T cd06309 87 DRGVDVKDDSLYVTFIGSDFVEEGRRAADWLAKATG-GKGNIVELQGTVGSSVAIDRKKGFAEVIKKYP 154 (273)
T ss_pred ecCcCCccCcceeeEecCChHHHHHHHHHHHHHHcC-CCceEEEEeCCCCCchHHHHHHHHHHHHHHCC
Confidence 75321 1221222322211111 23344445 67889998887665544455566677777763
No 63
>PRK09526 lacI lac repressor; Reviewed
Probab=57.36 E-value=61 Score=30.27 Aligned_cols=61 Identities=18% Similarity=0.261 Sum_probs=44.6
Q ss_pred cCCEEEEEEeCCCCCCcHHHHHHHHHHHHHcCCcEEEEEeCCCCHHH----HhcCc-CCccEEEEe
Q 042576 152 EARTWGIVLGTLGRQGNPRILERLQKRMEKKGFDYVVIMMSEISPAR----VALFE-DSVDAWIQI 212 (313)
Q Consensus 152 ~A~~~GIIvgTLg~Q~~~~ii~~l~~ll~~~Gkk~y~i~v~einp~K----Lanf~-~~ID~fV~i 212 (313)
..++||+|+..+....+..+++.+++.+++.|....++..++-++++ |.++. ..+|.+|+.
T Consensus 62 ~~~~Igvv~~~~~~~~~~~~~~gi~~~a~~~g~~~~i~~~~~~~~~~~~~~l~~l~~~~vdGiii~ 127 (342)
T PRK09526 62 QSLTIGLATTSLALHAPSQIAAAIKSRADQLGYSVVISMVERSGVEACQAAVNELLAQRVSGVIIN 127 (342)
T ss_pred CCceEEEEeCCCCcccHHHHHHHHHHHHHHCCCEEEEEeCCCChHHHHHHHHHHHHhcCCCEEEEe
Confidence 45789999998877777889999999999999887766555433322 33332 149998885
No 64
>cd06276 PBP1_FucR_like Ligand-binding domain of a transcription repressor, FucR, which functions as a molecular sensor of L-fucose availability. Ligand-binding domain of a transcription repressor, FucR, which functions as a molecular sensor of L-fucose availability. FcuR acts as an inducer of fucRRIAK and as a corepressor of another locus that regulates production of fucosylated glycans. FcuR and its close homologs in this group are a member of the LacI-GalR family repressors that are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes t
Probab=57.19 E-value=1.2e+02 Score=27.31 Aligned_cols=132 Identities=10% Similarity=0.040 Sum_probs=70.5
Q ss_pred ccHhHHHHHHHHHHhCC-CeEEecCCCCCCCc-cccCCCCCCCCCCCCCCeEEEecCCcccHHHHH-hhCCCceEEEeCC
Q 042576 47 QFASAIRAAKPELEKQG-FKVMIPQSKPLSAG-EVLGCTAPKIPARESDFNLVFIADGRFHLEAFM-ISNPGIKTFRYDP 123 (313)
Q Consensus 47 Qf~~~l~~~~~~L~~~g-~~v~ipq~~pls~G-evLGCt~~~~~~~~~~d~iv~igdGrFHle~~m-i~np~~~~y~yDP 123 (313)
-|...+..+.+.|+++| +++++..... ..- +++. ... ..+|++|+++.......-.. +....+|++.+|.
T Consensus 12 ~~~~~~~~i~~~l~~~g~~~l~~~~~~~-~~~~~~~~----~~~--~~vdGvIi~~~~~~~~~~~~~~~~~~~PvV~i~~ 84 (247)
T cd06276 12 FKEIIYNSFVNTLGKNAQVDLYFHHYNE-DLFKNIIS----NTK--GKYSGYVVMPHFKNEIQYFLLKKIPKEKLLILDH 84 (247)
T ss_pred HHHHHHHHHHHHHHhcCcEEEEEEcCch-HHHHHHHH----HHh--cCCCEEEEecCCCCcHHHHHHhccCCCCEEEEcC
Confidence 35566778888888899 8877632211 000 0110 001 23789888865322221222 2335678888885
Q ss_pred CC---CcccccccChHHHH-HHHHHHHHHHhhcCCEEEEEEeCCCCCCcHHHHHHHHHHHHHcCCcEE
Q 042576 124 YL---GKLFLEEYDNKGMR-ETRKRAIEKAMKEARTWGIVLGTLGRQGNPRILERLQKRMEKKGFDYV 187 (313)
Q Consensus 124 ys---~~~~~e~~d~~~~l-~~R~~~I~kak~~A~~~GIIvgTLg~Q~~~~ii~~l~~ll~~~Gkk~y 187 (313)
.. ..+.....|..+.- +.=..++++.+ .-+++|+|.|... .-...-.+-.++-++++|.+..
T Consensus 85 ~~~~~~~~~~V~~D~~~~~~~a~~~L~~~~~-G~~~Ia~i~~~~~-~~~~~R~~gf~~~l~~~g~~~~ 150 (247)
T cd06276 85 SIPEGGEYSSVAQDFEKAIYNALQEGLEKLK-KYKKLILVFPNKT-AIPKEIKRGFERFCKDYNIETE 150 (247)
T ss_pred cCCCCCCCCeEEEccHHHHHHHHHHHHHHhc-CCCEEEEEecCcc-HhHHHHHHHHHHHHHHcCCCcc
Confidence 42 12222334433221 11123444445 7789999987653 2233445666778888897643
No 65
>TIGR02417 fruct_sucro_rep D-fructose-responsive transcription factor. Members of this family belong the lacI helix-turn-helix family (pfam00356) of DNA-binding transcriptional regulators. All members are from the proteobacteria. Characterized members act as positive and negative transcriptional regulators of fructose and sucrose transport and metabolism. Sucrose is a disaccharide composed of fructose and glucose; D-fructose-1-phosphate rather than an intact sucrose moiety has been shown to act as the inducer.
Probab=57.19 E-value=64 Score=29.99 Aligned_cols=62 Identities=24% Similarity=0.489 Sum_probs=45.6
Q ss_pred cCCEEEEEEeCCCCCCcHHHHHHHHHHHHHcCCcEEEEEeCCCCHHH----HhcCc-CCccEEEEecC
Q 042576 152 EARTWGIVLGTLGRQGNPRILERLQKRMEKKGFDYVVIMMSEISPAR----VALFE-DSVDAWIQIAC 214 (313)
Q Consensus 152 ~A~~~GIIvgTLg~Q~~~~ii~~l~~ll~~~Gkk~y~i~v~einp~K----Lanf~-~~ID~fV~iaC 214 (313)
..+++|+|+..+.-..+..+++.+++.++++|....+...+. ++++ +..+. ..+|..|+.++
T Consensus 59 ~~~~Igvi~~~~~~~~~~~~~~~i~~~~~~~gy~~~i~~~~~-~~~~~~~~~~~l~~~~vdgiIi~~~ 125 (327)
T TIGR02417 59 RSRTIGLVIPDLENYSYARIAKELEQQCREAGYQLLIACSDD-NPDQEKVVIENLLARQVDALIVASC 125 (327)
T ss_pred CCceEEEEeCCCCCccHHHHHHHHHHHHHHCCCEEEEEeCCC-CHHHHHHHHHHHHHcCCCEEEEeCC
Confidence 457999999988878888999999999999998876655443 4433 22221 14999888765
No 66
>cd06281 PBP1_LacI_like_5 Ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. This group includes the ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.
Probab=56.96 E-value=39 Score=30.29 Aligned_cols=60 Identities=18% Similarity=0.284 Sum_probs=41.0
Q ss_pred EEEEEEeCCCCCCcHHHHHHHHHHHHHcCCcEEEEEeCCCCHHHHh----cCc-CCccEEEEecCC
Q 042576 155 TWGIVLGTLGRQGNPRILERLQKRMEKKGFDYVVIMMSEISPARVA----LFE-DSVDAWIQIACP 215 (313)
Q Consensus 155 ~~GIIvgTLg~Q~~~~ii~~l~~ll~~~Gkk~y~i~v~einp~KLa----nf~-~~ID~fV~iaCP 215 (313)
+||+|+....--.+..+++.+++.+++.|....+ ..+.-++++.. .+. ..+|++|+.+|.
T Consensus 1 ~Igvv~~~~~~~~~~~~~~~i~~~a~~~g~~~~~-~~~~~~~~~~~~~i~~l~~~~vdgii~~~~~ 65 (269)
T cd06281 1 TIGCLVSDITNPLLAQLFSGAEDRLRAAGYSLLI-ANSLNDPERELEILRSFEQRRMDGIIIAPGD 65 (269)
T ss_pred CEEEEecCCccccHHHHHHHHHHHHHHcCCEEEE-EeCCCChHHHHHHHHHHHHcCCCEEEEecCC
Confidence 4788888877777888888888888888877443 33444554322 221 148888888874
No 67
>PRK11041 DNA-binding transcriptional regulator CytR; Provisional
Probab=56.82 E-value=59 Score=29.78 Aligned_cols=62 Identities=11% Similarity=0.192 Sum_probs=45.0
Q ss_pred cCCEEEEEEeCCCCCCcHHHHHHHHHHHHHcCCcEEEEEeCCCCHHHH----hcC-cCCccEEEEecC
Q 042576 152 EARTWGIVLGTLGRQGNPRILERLQKRMEKKGFDYVVIMMSEISPARV----ALF-EDSVDAWIQIAC 214 (313)
Q Consensus 152 ~A~~~GIIvgTLg~Q~~~~ii~~l~~ll~~~Gkk~y~i~v~einp~KL----anf-~~~ID~fV~iaC 214 (313)
+.++||+|+..+.-.....+++.+++.+++.|....+..... +.++- ..+ ...+|++++.++
T Consensus 34 ~~~~ig~v~~~~~~~~~~~~~~gi~~~~~~~g~~~~~~~~~~-~~~~~~~~i~~l~~~~vDgiIi~~~ 100 (309)
T PRK11041 34 ESRTILVIVPDICDPFFSEIIRGIEVTAAEHGYLVLIGDCAH-QNQQEKTFVNLIITKQIDGMLLLGS 100 (309)
T ss_pred CCcEEEEEeCCCcCccHHHHHHHHHHHHHHCCCEEEEEeCCC-ChHHHHHHHHHHHHcCCCEEEEecC
Confidence 568999999888777888899999999999998776554332 33321 122 124999999865
No 68
>cd06315 PBP1_ABC_sugar_binding_like_6 Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems. Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily, which consists of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis.
Probab=56.67 E-value=38 Score=30.87 Aligned_cols=61 Identities=13% Similarity=0.031 Sum_probs=42.7
Q ss_pred CEEEEEEeCCCCCCcHHHHHHHHHHHHHcCCcEEEEEeCCCCHHHH----hcCc-CCccEEEEecCC
Q 042576 154 RTWGIVLGTLGRQGNPRILERLQKRMEKKGFDYVVIMMSEISPARV----ALFE-DSVDAWIQIACP 215 (313)
Q Consensus 154 ~~~GIIvgTLg~Q~~~~ii~~l~~ll~~~Gkk~y~i~v~einp~KL----anf~-~~ID~fV~iaCP 215 (313)
+++|+|+.++.-.....+++.+.+.+++.|....+. -+.-++++. .++. ..+|++|++++.
T Consensus 1 ~~ig~i~~~~~~~~~~~~~~gi~~~a~~~gy~~~~~-~~~~~~~~~~~~i~~l~~~~vdgiil~~~~ 66 (280)
T cd06315 1 KNIIFVASDLKNGGILGVGEGVREAAKAIGWNLRIL-DGRGSEAGQAAALNQAIALKPDGIVLGGVD 66 (280)
T ss_pred CeEEEEecccCCcHHHHHHHHHHHHHHHcCcEEEEE-CCCCCHHHHHHHHHHHHHcCCCEEEEcCCC
Confidence 578999998888788889999999999998664333 344455442 2221 148999988754
No 69
>cd06316 PBP1_ABC_sugar_binding_like_7 Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems. Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily, which consists of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis.
Probab=56.58 E-value=19 Score=33.08 Aligned_cols=61 Identities=20% Similarity=0.231 Sum_probs=33.8
Q ss_pred EEEEEEeCCCCCCcHHHHHHHHHHHHHcCCcEEEEEeCCCCHHHHh----cC-cCCccEEEEecCC
Q 042576 155 TWGIVLGTLGRQGNPRILERLQKRMEKKGFDYVVIMMSEISPARVA----LF-EDSVDAWIQIACP 215 (313)
Q Consensus 155 ~~GIIvgTLg~Q~~~~ii~~l~~ll~~~Gkk~y~i~v~einp~KLa----nf-~~~ID~fV~iaCP 215 (313)
++|+|+.++.-.....+++.+++.+++.|.....+.-++-++++.. .+ ...+|++|+.++.
T Consensus 1 ~i~~i~~~~~~~~~~~~~~gi~~~a~~~g~~~~~~~~~~~~~~~~~~~l~~~~~~~~dgiii~~~~ 66 (294)
T cd06316 1 KAAIVMHTSGSDWSNAQVRGAKDEFAKLGIEVVATTDAQFDPAKQVADIETTISQKPDIIISIPVD 66 (294)
T ss_pred CeEEEecCCCChHHHHHHHHHHHHHHHcCCEEEEecCCCCCHHHHHHHHHHHHHhCCCEEEEcCCC
Confidence 3677776654444445666777777777766543333444554321 11 1247777776664
No 70
>PRK07308 flavodoxin; Validated
Probab=56.29 E-value=51 Score=27.53 Aligned_cols=57 Identities=16% Similarity=0.161 Sum_probs=42.4
Q ss_pred EEEEEEeCCCCCCcHHHHHHHHHHHHHcCCcEEEEEeCCCCHHHHhcCcCCccEEEEecCCCc
Q 042576 155 TWGIVLGTLGRQGNPRILERLQKRMEKKGFDYVVIMMSEISPARVALFEDSVDAWIQIACPRL 217 (313)
Q Consensus 155 ~~GIIvgTLg~Q~~~~ii~~l~~ll~~~Gkk~y~i~v~einp~KLanf~~~ID~fV~iaCPrl 217 (313)
++-||.+|.. -+...+++.|.+.|++.|..+.+.-+.+..+..|. +.|++|+ +||--
T Consensus 3 ~~~IvY~S~t-GnTe~iA~~ia~~l~~~g~~~~~~~~~~~~~~~l~----~~d~vi~-g~~t~ 59 (146)
T PRK07308 3 LAKIVYASMT-GNTEEIADIVADKLRELGHDVDVDECTTVDASDFE----DADIAIV-ATYTY 59 (146)
T ss_pred eEEEEEECCC-chHHHHHHHHHHHHHhCCCceEEEecccCCHhHhc----cCCEEEE-EeCcc
Confidence 5778999943 34556899999999999998888888888776654 3566544 88763
No 71
>cd06299 PBP1_LacI_like_13 Ligand-binding domain of DNA-binding regulatory protein from Corynebacterium glutamicum which has a unique ability to produce significant amounts of L-glutamate directly from cheap sugar and ammonia. This group includes the ligand-binding domain of DNA-binding regulatory protein from Corynebacterium glutamicum which has a unique ability to produce significant amounts of L-glutamate directly from cheap sugar and ammonia. This regulatory protein is a member of the LacI-GalR family of bacterial transcription repressors. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial trans
Probab=56.22 E-value=37 Score=30.12 Aligned_cols=60 Identities=13% Similarity=0.206 Sum_probs=33.6
Q ss_pred EEEEEEeCCCCCCcHHHHHHHHHHHHHcCCcEEEEEeCCCCHHHH----hcC-cCCccEEEEecCC
Q 042576 155 TWGIVLGTLGRQGNPRILERLQKRMEKKGFDYVVIMMSEISPARV----ALF-EDSVDAWIQIACP 215 (313)
Q Consensus 155 ~~GIIvgTLg~Q~~~~ii~~l~~ll~~~Gkk~y~i~v~einp~KL----anf-~~~ID~fV~iaCP 215 (313)
+||+|+..+.--.+..+++.+++.+++.|....++... -++++. ..+ ...+|++|+.++.
T Consensus 1 ~igvv~~~~~~~~~~~~~~gi~~~~~~~g~~~~~~~~~-~~~~~~~~~~~~l~~~~vdgiIi~~~~ 65 (265)
T cd06299 1 TIGVIVPDIRNPYFASLATAIQDAASAAGYSTIIGNSD-ENPETENRYLDNLLSQRVDGIIVVPHE 65 (265)
T ss_pred CEEEEecCCCCccHHHHHHHHHHHHHHcCCEEEEEeCC-CCHHHHHHHHHHHHhcCCCEEEEcCCC
Confidence 36777766655566667777777777777655554332 233321 111 1137777776654
No 72
>PRK10423 transcriptional repressor RbsR; Provisional
Probab=55.81 E-value=60 Score=30.04 Aligned_cols=62 Identities=15% Similarity=0.287 Sum_probs=45.5
Q ss_pred cCCEEEEEEeCCCCCCcHHHHHHHHHHHHHcCCcEEEEEeCCCCHHH----HhcCc-CCccEEEEecC
Q 042576 152 EARTWGIVLGTLGRQGNPRILERLQKRMEKKGFDYVVIMMSEISPAR----VALFE-DSVDAWIQIAC 214 (313)
Q Consensus 152 ~A~~~GIIvgTLg~Q~~~~ii~~l~~ll~~~Gkk~y~i~v~einp~K----Lanf~-~~ID~fV~iaC 214 (313)
..+++|+|+..+.-..+..+++.+++.+++.|.+..+.. ..-++++ |.+|. ..+|.+|+.+.
T Consensus 55 ~~~~Igvi~~~~~~~~~~~~~~gi~~~~~~~g~~~~~~~-~~~~~~~~~~~~~~l~~~~vdGiI~~~~ 121 (327)
T PRK10423 55 QTRTIGMLITASTNPFYSELVRGVERSCFERGYSLVLCN-TEGDEQRMNRNLETLMQKRVDGLLLLCT 121 (327)
T ss_pred CCCeEEEEeCCCCCCcHHHHHHHHHHHHHHcCCEEEEEe-CCCCHHHHHHHHHHHHHcCCCEEEEeCC
Confidence 567999999988888899999999999999997765543 3334443 22231 24999998764
No 73
>PF00532 Peripla_BP_1: Periplasmic binding proteins and sugar binding domain of LacI family; InterPro: IPR001761 This family includes the periplasmic binding proteins, and the LacI family transcriptional regulators. The periplasmic binding proteins are the primary receptors for chemotaxis and transport of many sugar based solutes. The LacI family of proteins consist of transcriptional regulators related to the lac repressor. In this case, generally the sugar binding domain binds a sugar which changes the DNA binding activity of the repressor domain (lacI) [, ].; PDB: 1BAP_A 7ABP_A 6ABP_A 1ABF_A 5ABP_A 2WRZ_B 9ABP_A 1APB_A 1ABE_A 8ABP_A ....
Probab=55.75 E-value=38 Score=31.63 Aligned_cols=61 Identities=13% Similarity=0.262 Sum_probs=44.7
Q ss_pred CEEEEEEeCCCCCCcHHHHHHHHHHHHHcCCcEEEEEeCCCCHHHHh---cCc-CCccEEEEecCC
Q 042576 154 RTWGIVLGTLGRQGNPRILERLQKRMEKKGFDYVVIMMSEISPARVA---LFE-DSVDAWIQIACP 215 (313)
Q Consensus 154 ~~~GIIvgTLg~Q~~~~ii~~l~~ll~~~Gkk~y~i~v~einp~KLa---nf~-~~ID~fV~iaCP 215 (313)
+++|+|+..+.-....++++-|++.++++|....++..+ =++++-. .+. ..||.+|+.+..
T Consensus 2 ~~IGvivp~~~npff~~ii~gIe~~a~~~Gy~l~l~~t~-~~~~~e~~i~~l~~~~vDGiI~~s~~ 66 (279)
T PF00532_consen 2 KTIGVIVPDISNPFFAEIIRGIEQEAREHGYQLLLCNTG-DDEEKEEYIELLLQRRVDGIILASSE 66 (279)
T ss_dssp CEEEEEESSSTSHHHHHHHHHHHHHHHHTTCEEEEEEET-TTHHHHHHHHHHHHTTSSEEEEESSS
T ss_pred CEEEEEECCCCCcHHHHHHHHHHHHHHHcCCEEEEecCC-CchHHHHHHHHHHhcCCCEEEEeccc
Confidence 689999999998899999999999999999877665544 3344322 111 149999988443
No 74
>PRK02048 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; Provisional
Probab=55.13 E-value=1.3e+02 Score=32.10 Aligned_cols=141 Identities=20% Similarity=0.235 Sum_probs=81.4
Q ss_pred CChHHHHHHHHHhCCCCCeEEEE--eccccHhHHHHHHHHHHhCCCeEEecCCCCCCCccccCCCCCCCCCCCCCCeEEE
Q 042576 21 IDVNRLIDTIKVNYSDPGKLILA--GTIQFASAIRAAKPELEKQGFKVMIPQSKPLSAGEVLGCTAPKIPARESDFNLVF 98 (313)
Q Consensus 21 iD~~~~i~~i~~~f~~~~~i~Lv--~tiQf~~~l~~~~~~L~~~g~~v~ipq~~pls~GevLGCt~~~~~~~~~~d~iv~ 98 (313)
-|++..++++++....+..|+=+ =+.+-+.++..+++.|+..|+++ | .
T Consensus 38 ~D~~atv~Qi~~l~~aGceiVRvtv~~~~~a~~l~~I~~~l~~~G~~i------------------P------------L 87 (611)
T PRK02048 38 MDTEACVAQAKRIIDAGGEYVRLTTQGVREAENLMNINIGLRSQGYMV------------------P------------L 87 (611)
T ss_pred ccHHHHHHHHHHHHHcCCCEEEEcCCCHHHHHhHHHHHHHHhhcCCCC------------------C------------E
Confidence 47788888888776655544432 24567777888888888777652 1 2
Q ss_pred ecCCcccHHHHHhhCCCceEEEeCCCCC----------cccccccCh--HHHHHHHHHHHHHHhhcCCEEEEEEeCCCCC
Q 042576 99 IADGRFHLEAFMISNPGIKTFRYDPYLG----------KLFLEEYDN--KGMRETRKRAIEKAMKEARTWGIVLGTLGRQ 166 (313)
Q Consensus 99 igdGrFHle~~mi~np~~~~y~yDPys~----------~~~~e~~d~--~~~l~~R~~~I~kak~~A~~~GIIvgTLg~Q 166 (313)
|+|-.|...-++.+-....-+|.||=+- ..|.|+|.. +++..+-...|++|| +.+ +.|=+|+-.|.
T Consensus 88 VADIHF~~~~A~~a~~~v~kiRINPGN~~~~~k~f~~~~Ytdeey~~el~~i~e~~~~~v~~ak-~~~-~~iRIGvN~GS 165 (611)
T PRK02048 88 VADVHFNPKVADVAAQYAEKVRINPGNYVDPGRTFKKLEYTDEEYAQEIQKIRDRFVPFLNICK-ENH-TAIRIGVNHGS 165 (611)
T ss_pred EEecCCCcHHHHHHHHhhCCEEECCCcCCCccccccccccchhhhhhhhhhHHHHHHHHHHHHH-HCC-CCEEEecCCcC
Confidence 4444555433443333466778887322 234555542 333344466788888 533 33444554444
Q ss_pred CcHHHHHHH--------------HHHHHHcCCcEEEEEeCC
Q 042576 167 GNPRILERL--------------QKRMEKKGFDYVVIMMSE 193 (313)
Q Consensus 167 ~~~~ii~~l--------------~~ll~~~Gkk~y~i~v~e 193 (313)
-...++++. -+++++.|..-++|+|--
T Consensus 166 L~~~i~~~yg~tpe~mVeSAle~~~i~e~~~f~diviS~Ks 206 (611)
T PRK02048 166 LSDRIMSRYGDTPEGMVESCMEFLRICVEEHFTDVVISIKA 206 (611)
T ss_pred chHHHHHHhCCChHHHHHHHHHHHHHHHHCCCCcEEEEEEe
Confidence 444444432 345777888777777753
No 75
>COG5623 CLP1 Predicted GTPase subunit of the pre-mRNA cleavage complex [Translation, ribosomal structure and biogenesis]
Probab=54.72 E-value=67 Score=31.83 Aligned_cols=169 Identities=14% Similarity=0.185 Sum_probs=87.0
Q ss_pred CChHHHHHHHH-HhCCCCCeEEEEeccccHhH--HHHHHH-HHHhCCCeEEecCCCCCCCcccc-CCCCCCCCCCCCCCe
Q 042576 21 IDVNRLIDTIK-VNYSDPGKLILAGTIQFASA--IRAAKP-ELEKQGFKVMIPQSKPLSAGEVL-GCTAPKIPARESDFN 95 (313)
Q Consensus 21 iD~~~~i~~i~-~~f~~~~~i~Lv~tiQf~~~--l~~~~~-~L~~~g~~v~ipq~~pls~GevL-GCt~~~~~~~~~~d~ 95 (313)
+++..+++.++ .|++.+.++.+++.-|--.. ...+-. +|+ .++..+.-..+|..||-++ ||-+.. + +++
T Consensus 82 ~Nlhf~lek~rm~n~e~gp~v~vvGgsq~Gkts~~~tL~syalk-~~~~pl~~nlDP~Qp~~~~PG~iSa~-h----~~~ 155 (424)
T COG5623 82 FNLHFFLEKRRMFNYEKGPTVMVVGGSQNGKTSFCFTLISYALK-LGKKPLFTNLDPSQPGNIFPGAISAI-H----VDA 155 (424)
T ss_pred hhHHHHHHhhcccccccCCEEEEECCCcCCceeHHHHHHHHHHH-hcCCceEEecCCCCcccccCcccccc-c----hhh
Confidence 35667788888 68887888999984443221 122222 233 2566555556777777765 565432 2 122
Q ss_pred EEEecCCccc------HHHHHhhCCCceEEEeCCCCCcccccccChHHHHHHHHHHHHHHhh----cCCEEEEEEeCCCC
Q 042576 96 LVFIADGRFH------LEAFMISNPGIKTFRYDPYLGKLFLEEYDNKGMRETRKRAIEKAMK----EARTWGIVLGTLGR 165 (313)
Q Consensus 96 iv~igdGrFH------le~~mi~np~~~~y~yDPys~~~~~e~~d~~~~l~~R~~~I~kak~----~A~~~GIIvgTLg~ 165 (313)
++=.-+|.|- +..+..-+|-..-|-.|--+ |..+.-.+--.|....-++|. +++..|-+++|-+.
T Consensus 156 ilD~q~~~wGqSltsGaTll~~K~Plv~nfGl~~i~-----eN~~LY~l~~s~L~~aV~~r~hl~~d~r~sgC~vdTpSI 230 (424)
T COG5623 156 ILDCQEGLWGQSLTSGATLLRLKNPLVFNFGLTEIT-----ENMELYDLQTSKLQEAVKARNHLVEDLRLSGCPVDTPSI 230 (424)
T ss_pred hhhhhcccccccccccchhhhccCceEEecccCccc-----cCHHHHHHHHHHHHHHHHhhhccCccceeecCccCCcch
Confidence 2222222211 11233334322222222111 111111122233333334431 57899999999876
Q ss_pred CCcHH-HHHHHHHHHHHcCCcEEEEEeCCCCHHHHh
Q 042576 166 QGNPR-ILERLQKRMEKKGFDYVVIMMSEISPARVA 200 (313)
Q Consensus 166 Q~~~~-ii~~l~~ll~~~Gkk~y~i~v~einp~KLa 200 (313)
|..-+ +.+-...+|++-.....+++-+|---.+|.
T Consensus 231 sqldEnla~~~htiI~~f~vnivvVlgsErLy~s~k 266 (424)
T COG5623 231 SQLDENLAAFYHTIIKRFEVNIVVVLGSERLYHSLK 266 (424)
T ss_pred hhhhHHHHHHHHHHHHheeeeEEEEEcchHHHHHHH
Confidence 66554 444444477777777777777775555554
No 76
>cd06291 PBP1_Qymf_like Ligand binding domain of the lacI-like transcription regulator from a novel metal-reducing bacterium Alkaliphilus Metalliredigens (strain Qymf) and its close homologs. This group includes the ligand binding domain of the lacI-like transcription regulator from a novel metal-reducing bacterium Alkaliphilus Metalliredigens (strain Qymf) and its close homologs. Qymf is a strict anaerobe that could be grown in the presence of borax and its cells are straight rods that produce endospores. This group is a member of the LacI-GalR family repressors that are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription
Probab=53.86 E-value=39 Score=30.06 Aligned_cols=60 Identities=17% Similarity=0.304 Sum_probs=35.5
Q ss_pred EEEEEEeCCCCCCcHHHHHHHHHHHHHcCCcEEEEEeCCCCHHHHhcC-----cCCccEEEEecCC
Q 042576 155 TWGIVLGTLGRQGNPRILERLQKRMEKKGFDYVVIMMSEISPARVALF-----EDSVDAWIQIACP 215 (313)
Q Consensus 155 ~~GIIvgTLg~Q~~~~ii~~l~~ll~~~Gkk~y~i~v~einp~KLanf-----~~~ID~fV~iaCP 215 (313)
+||+|+..+..-....+++.+++.+++.|.+..++.. +-++++-..+ ...+|++|..++.
T Consensus 1 ~I~vi~~~~~~~~~~~~~~gi~~~~~~~g~~~~~~~~-~~~~~~~~~~i~~~~~~~~dgiii~~~~ 65 (265)
T cd06291 1 LIGLIVPTISNPFFSELARAVEKELYKKGYKLILCNS-DNDPEKEREYLEMLRQNQVDGIIAGTHN 65 (265)
T ss_pred CEEEEECCCCChhHHHHHHHHHHHHHHCCCeEEEecC-CccHHHHHHHHHHHHHcCCCEEEEecCC
Confidence 3677777777667777777777777777766543322 2233322111 1137777777663
No 77
>PRK00087 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/S1 RNA-binding domain protein; Reviewed
Probab=53.79 E-value=1.1e+02 Score=32.61 Aligned_cols=118 Identities=18% Similarity=0.206 Sum_probs=70.8
Q ss_pred CCCCCeEEEEe-ccccHhHHHHHHHHHHhCCCeEEecCCCCCCCccccCCCCCCCCC------CCCCCeEEEecCCc---
Q 042576 34 YSDPGKLILAG-TIQFASAIRAAKPELEKQGFKVMIPQSKPLSAGEVLGCTAPKIPA------RESDFNLVFIADGR--- 103 (313)
Q Consensus 34 f~~~~~i~Lv~-tiQf~~~l~~~~~~L~~~g~~v~ipq~~pls~GevLGCt~~~~~~------~~~~d~iv~igdGr--- 103 (313)
++..+++++++ |.|-....+.+.+.|+.+++++.+. ..| |.+..... ...+|++++||+-.
T Consensus 150 ~~~~~~~~~~~QTT~~~~~~~~~~~~l~~~~~~~~~~-------~ti--C~at~~Rq~a~~~la~~~d~~~vvGg~~SsN 220 (647)
T PRK00087 150 LPFDKKICVVSQTTEKQENFEKVLKELKKKGKEVKVF-------NTI--CNATEVRQEAAEKLAKKVDVMIVVGGKNSSN 220 (647)
T ss_pred CCCCCCEEEEEcCCCcHHHHHHHHHHHHHhCCCcccC-------CCc--chhhhhHHHHHHHHHhhCCEEEEECCCCCcc
Confidence 33346788775 7788888999999999888776542 223 44432110 02489999998743
Q ss_pred -ccHHHHHhhCCCceEEEeCCCCCcccccccChHHHHHHHHHHHHHHhhcCCEEEEEEeCCCCCCcHHHHHHHHHHHHHc
Q 042576 104 -FHLEAFMISNPGIKTFRYDPYLGKLFLEEYDNKGMRETRKRAIEKAMKEARTWGIVLGTLGRQGNPRILERLQKRMEKK 182 (313)
Q Consensus 104 -FHle~~mi~np~~~~y~yDPys~~~~~e~~d~~~~l~~R~~~I~kak~~A~~~GIIvgTLg~Q~~~~ii~~l~~ll~~~ 182 (313)
-||..+.-.. ..++|..+-.+ +.+. +..+ +++++||.-|+ .---++++.+...|++.
T Consensus 221 t~~L~~i~~~~-~~~~~~ie~~~------el~~-----------~~~~-~~~~vgitaga---StP~~~i~~v~~~l~~~ 278 (647)
T PRK00087 221 TTKLYEICKSN-CTNTIHIENAG------ELPE-----------EWFK-GVKIIGVTAGA---STPDWIIEEVIKKMSEL 278 (647)
T ss_pred HHHHHHHHHHH-CCCEEEECChH------HCCH-----------HHhC-CCCEEEEEecc---CCCHHHHHHHHHHHHHh
Confidence 2455555432 35677665332 2221 2345 78899998876 33344666666555543
No 78
>PRK10703 DNA-binding transcriptional repressor PurR; Provisional
Probab=53.77 E-value=31 Score=32.31 Aligned_cols=62 Identities=13% Similarity=0.237 Sum_probs=44.9
Q ss_pred cCCEEEEEEeCCCCCCcHHHHHHHHHHHHHcCCcEEEEEeCCCCHHHHh----cCc-CCccEEEEecC
Q 042576 152 EARTWGIVLGTLGRQGNPRILERLQKRMEKKGFDYVVIMMSEISPARVA----LFE-DSVDAWIQIAC 214 (313)
Q Consensus 152 ~A~~~GIIvgTLg~Q~~~~ii~~l~~ll~~~Gkk~y~i~v~einp~KLa----nf~-~~ID~fV~iaC 214 (313)
..+++|+|+..+.......+++.+++.+++.|.+.+++.. .-++++.. .+. ..+|++|+.+.
T Consensus 58 ~~~~i~vi~~~~~~~~~~~~~~gi~~~~~~~g~~~~~~~~-~~~~~~~~~~i~~l~~~~vdgiii~~~ 124 (341)
T PRK10703 58 HTKSIGLLATSSEAPYFAEIIEAVEKNCYQKGYTLILCNA-WNNLEKQRAYLSMLAQKRVDGLLVMCS 124 (341)
T ss_pred CCCeEEEEeCCCCCchHHHHHHHHHHHHHHCCCEEEEEeC-CCCHHHHHHHHHHHHHcCCCEEEEecC
Confidence 4579999999988888888999999999999987665543 33454432 121 14899987664
No 79
>PRK05723 flavodoxin; Provisional
Probab=53.73 E-value=51 Score=28.40 Aligned_cols=55 Identities=13% Similarity=0.147 Sum_probs=40.1
Q ss_pred EEEEEEeCCCCCCcHHHHHHHHHHHHHcCCcEEEEEeCCCCHHHHhcCcCCccEEEEecCC
Q 042576 155 TWGIVLGTLGRQGNPRILERLQKRMEKKGFDYVVIMMSEISPARVALFEDSVDAWIQIACP 215 (313)
Q Consensus 155 ~~GIIvgTLg~Q~~~~ii~~l~~ll~~~Gkk~y~i~v~einp~KLanf~~~ID~fV~iaCP 215 (313)
+++|+.||-.+ ....+.++|.+.|.+.|.+..+ +.+.+++.|..++ .|.. ++.|+
T Consensus 2 ~i~I~ygS~tG-~ae~~A~~la~~l~~~g~~~~~--~~~~~~~~~~~~~--~~~l-i~~~s 56 (151)
T PRK05723 2 KVAILSGSVYG-TAEEVARHAESLLKAAGFEAWH--NPRASLQDLQAFA--PEAL-LAVTS 56 (151)
T ss_pred eEEEEEEcCch-HHHHHHHHHHHHHHHCCCceee--cCcCCHhHHHhCC--CCeE-EEEEC
Confidence 68999999764 3456999999999999988765 3457788888775 4554 33343
No 80
>PF00919 UPF0004: Uncharacterized protein family UPF0004; InterPro: IPR013848 The methylthiotransferase (MTTase) or miaB-like family is named after the (dimethylallyl)adenosine tRNA MTTase miaB protein, which catalyses a C-H to C-S bond conversion in the methylthiolation of tRNA. A related bacterial enzyme rimO performs a similar methylthiolation, but on a protein substrate. RimO acts on the ribosomal protein S12 and forms a separate MTTase subfamily. The miaB-subfamily includes mammalian CDK5 regulatory subunit-associated proteins and similar proteins in other eukaryotes. Two other subfamilies, yqeV and CDKAL1, are named after a Bacillus subtilis and a human protein, respectively. While yqeV-like proteins are found in bacteria, CDKAL1 subfamily members occur in eukaryotes and in archaebacteria. The likely MTTases from these 4 subfamilies contain an N-terminal MTTase domain, a central radical generating fold and a C-terminal TRAM domain (see PDOC50926 from PROSITEDOC). The core forms a radical SAM fold (or AdoMet radical), containing a cysteine motif CxxxCxxC that binds a [4Fe-4S] cluster [, , ]. A reducing equivalent from the [4Fe-4S]+ cluster is used to cleave S-adenosylmethionine (SAM) to generate methionine and a 5'-deoxyadenosyl radical. The latter is thought to produce a reactive substrate radical that is amenable to sulphur insertion [, ]. The N-terminal MTTase domain contains 3 cysteines that bind a second [4Fe-4S] cluster, in addition to the radical-generating [4Fe-4S] cluster, which could be involved in the thiolation reaction. The C-terminal TRAM domain is not shared with other radical SAM proteins outside the MTTase family. The TRAM domain can bind to RNA substrate and seems to be important for substrate recognition. The tertiary structure of the central radical SAM fold has six beta/alpha motifs resembling a three-quarter TIM barrel core (see PDOC00155 from PROSITEDOC) []. The N-terminal MTTase domain might form an additional [beta/alpha]2 TIM barrel unit []. ; GO: 0003824 catalytic activity, 0051539 4 iron, 4 sulfur cluster binding, 0009451 RNA modification
Probab=53.67 E-value=44 Score=26.81 Aligned_cols=64 Identities=14% Similarity=0.063 Sum_probs=44.4
Q ss_pred HHHHhhcCCEEEEEEeCCCCCCcHHHHHHHHHHHHHcCCcEEEEEeC---CCCHHHHhcCcCCccEEE
Q 042576 146 IEKAMKEARTWGIVLGTLGRQGNPRILERLQKRMEKKGFDYVVIMMS---EISPARVALFEDSVDAWI 210 (313)
Q Consensus 146 I~kak~~A~~~GIIvgTLg~Q~~~~ii~~l~~ll~~~Gkk~y~i~v~---einp~KLanf~~~ID~fV 210 (313)
++... +|..+-|--.|.--+--.+++++|+++.+.......+++.| +..+++|.....++|+|+
T Consensus 31 ~~~~e-~AD~iiiNTC~V~~~Ae~k~~~~i~~l~~~~~~~~~ivv~GC~aq~~~~~l~~~~p~vd~v~ 97 (98)
T PF00919_consen 31 VDDPE-EADVIIINTCTVRESAEQKSRNRIRKLKKLKKPGAKIVVTGCMAQRYGEELKKEFPEVDLVV 97 (98)
T ss_pred ecccc-cCCEEEEEcCCCCcHHHHHHHHHHHHHHHhcCCCCEEEEEeCccccChHHHHhhCCCeEEEe
Confidence 33345 78887666666655566678888888887764556666666 777888887653789875
No 81
>PF00258 Flavodoxin_1: Flavodoxin; InterPro: IPR008254 This domain is found in a number of proteins including flavodoxin and nitric-oxide synthase. Flavodoxins are electron-transfer proteins that function in various electron transport systems. They bind one FMN molecule, which serves as a redox-active prosthetic group [] and are functionally interchangeable with ferredoxins. They have been isolated from prokaryotes, cyanobacteria, and some eukaryotic algae. Nitric oxide synthase (1.14.13.39 from EC) produces nitric oxide from L-arginie and NADPH. Nitric oxide acts as a messenger molecule in the body.; GO: 0010181 FMN binding, 0016491 oxidoreductase activity; PDB: 2WC1_A 2FVX_A 2FOX_A 6NUL_A 1FVX_A 2FAX_A 1FLN_A 1FLA_A 4NLL_A 2FDX_A ....
Probab=53.51 E-value=33 Score=28.21 Aligned_cols=54 Identities=15% Similarity=0.350 Sum_probs=38.6
Q ss_pred EEEeCCCCCCcHHHHHHHHHHHHHcCCcEEEEEeCCCCHHHHhcCcCCccEEEEecCC
Q 042576 158 IVLGTLGRQGNPRILERLQKRMEKKGFDYVVIMMSEISPARVALFEDSVDAWIQIACP 215 (313)
Q Consensus 158 IIvgTLg~Q~~~~ii~~l~~ll~~~Gkk~y~i~v~einp~KLanf~~~ID~fV~iaCP 215 (313)
|+-+|.. -+...+++.|.+.|+++|.++.++-+.+.+.. +..+. +-+.+| +.||
T Consensus 1 I~Y~S~t-G~te~~A~~ia~~l~~~g~~~~~~~~~~~~~~-~~~~~-~~~~~i-~~~s 54 (143)
T PF00258_consen 1 IVYGSMT-GNTEKMAEAIAEGLRERGVEVRVVDLDDFDDS-PSDLS-EYDLLI-FGVS 54 (143)
T ss_dssp EEEETSS-SHHHHHHHHHHHHHHHTTSEEEEEEGGGSCHH-HHHHC-TTSEEE-EEEE
T ss_pred CEEECCc-hhHHHHHHHHHHHHHHcCCceeeechhhhhhh-hhhhh-hhceee-Eeec
Confidence 5666654 23457999999999999999999999999976 33444 344544 4444
No 82
>PF06180 CbiK: Cobalt chelatase (CbiK); InterPro: IPR010388 This group, typified by Salmonella typhimurium CbiK, contains anaerobic cobalt chelatases that act in the anaerobic cobalamin biosynthesis pathway [, ]. Cobalamin (vitamin B12) can be complexed with metal via ATP-dependent reactions (aerobic pathway) (e.g., in Pseudomonas denitrificans) or via ATP-independent reactions (anaerobic pathway) (e.g., in S. typhimurium) [, ]. The corresponding cobalt chelatases are not homologous. This group belongs to the class of ATP-independent, single-subunit chelatases that also includes distantly related protoporphyrin IX (PPIX) ferrochelatase (HemH) (Class II chelatases) []. The structure of S. typhimurium CbiK shows that it has a remarkably similar topology to Bacillus subtilis ferrochelatase despite only weak sequence conservation []. Both enzymes contain a histidine residue identified as the metal ion ligand, but CbiK contains a second histidine in place of the glutamic acid residue identified as a general base in PPIX ferrochelatase []. Site-directed mutagenesis has confirmed a role for this histidine and a nearby glutamic acid in cobalt binding, modulating metal ion specificity as well as catalytic efficiency []. It should be noted that CysG and Met8p, which are multifunctional proteins associated with siroheme biosynthesis, include chelatase activity and can therefore be considered as the third class of chelatases []. As with the class II chelatases, they do not require ATP for activity. However, they are not structurally similar to HemH or CbiK, and it is likely that they have arisen by the acquisition of a chelatase function within a dehydrogenase catalytic framework [, ].; GO: 0016852 sirohydrochlorin cobaltochelatase activity; PDB: 1QGO_A 2XWP_A 2XVZ_A 2XVX_A 2XVY_A.
Probab=53.16 E-value=1.9e+02 Score=27.36 Aligned_cols=15 Identities=27% Similarity=0.388 Sum_probs=9.4
Q ss_pred CCeEEEecCCcccHH
Q 042576 93 DFNLVFIADGRFHLE 107 (313)
Q Consensus 93 ~d~iv~igdGrFHle 107 (313)
.+++||+|.|.-|..
T Consensus 141 ~~a~vlmGHGt~h~a 155 (262)
T PF06180_consen 141 DEAVVLMGHGTPHPA 155 (262)
T ss_dssp TEEEEEEE---SCHH
T ss_pred CCEEEEEeCCCCCCc
Confidence 478999999998853
No 83
>PRK11303 DNA-binding transcriptional regulator FruR; Provisional
Probab=53.11 E-value=1.9e+02 Score=26.74 Aligned_cols=148 Identities=9% Similarity=0.050 Sum_probs=71.6
Q ss_pred eEEEEec----cccHhHHHHHHHHHHhCCCeEEecCC--CCCCCccccCCCCCCCCCCCCCCeEEEecCC-cccHHHHHh
Q 042576 39 KLILAGT----IQFASAIRAAKPELEKQGFKVMIPQS--KPLSAGEVLGCTAPKIPARESDFNLVFIADG-RFHLEAFMI 111 (313)
Q Consensus 39 ~i~Lv~t----iQf~~~l~~~~~~L~~~g~~v~ipq~--~pls~GevLGCt~~~~~~~~~~d~iv~igdG-rFHle~~mi 111 (313)
.|+++.. --|...++.+.+.+++.|+++++-.. .+...-+.+. .... ..+|++|+.+.- .....--.+
T Consensus 63 ~Igvv~~~~~~~~~~~l~~gi~~~~~~~g~~~~~~~~~~~~~~~~~~~~---~l~~--~~vdgiIi~~~~~~~~~~~~~l 137 (328)
T PRK11303 63 SIGLIIPDLENTSYARIAKYLERQARQRGYQLLIACSDDQPDNEMRCAE---HLLQ--RQVDALIVSTSLPPEHPFYQRL 137 (328)
T ss_pred eEEEEeCCCCCchHHHHHHHHHHHHHHcCCEEEEEeCCCCHHHHHHHHH---HHHH--cCCCEEEEcCCCCCChHHHHHH
Confidence 4776642 23555667788889999999765221 1100001110 0001 137888876531 112111122
Q ss_pred hCCCceEEEeCCCCC--cccccccChHHHHHHH--HHHHHHHhhcCCEEEEEEeCCCCCCcHHHHHHHHHHHHHcCCcEE
Q 042576 112 SNPGIKTFRYDPYLG--KLFLEEYDNKGMRETR--KRAIEKAMKEARTWGIVLGTLGRQGNPRILERLQKRMEKKGFDYV 187 (313)
Q Consensus 112 ~np~~~~y~yDPys~--~~~~e~~d~~~~l~~R--~~~I~kak~~A~~~GIIvgTLg~Q~~~~ii~~l~~ll~~~Gkk~y 187 (313)
..-.+|++.+|.... .+.....|.... ..+ .+++ .+ ..+++|+|-|.........-.+-.++-++++|....
T Consensus 138 ~~~~iPvV~v~~~~~~~~~~~V~~d~~~~-~~~a~~~L~--~~-G~r~I~~i~~~~~~~~~~~R~~Gf~~al~~~g~~~~ 213 (328)
T PRK11303 138 QNDGLPIIALDRALDREHFTSVVSDDQDD-AEMLAESLL--KF-PAESILLLGALPELSVSFEREQGFRQALKDDPREVH 213 (328)
T ss_pred HhcCCCEEEECCCCCCCCCCEEEeCCHHH-HHHHHHHHH--HC-CCCeEEEEeCccccccHHHHHHHHHHHHHHcCCCce
Confidence 334678888875421 111112232211 111 1122 23 568999997754433333344556777888887654
Q ss_pred EEEeCCCC
Q 042576 188 VIMMSEIS 195 (313)
Q Consensus 188 ~i~v~ein 195 (313)
.+..+..+
T Consensus 214 ~~~~~~~~ 221 (328)
T PRK11303 214 YLYANSFE 221 (328)
T ss_pred EEEeCCCC
Confidence 44444444
No 84
>PRK09526 lacI lac repressor; Reviewed
Probab=51.94 E-value=2e+02 Score=26.73 Aligned_cols=150 Identities=10% Similarity=0.086 Sum_probs=74.7
Q ss_pred eEEEEe-cc---ccHhHHHHHHHHHHhCCCeEEecCCCCCCC-c--cccCCCCCCCCCCCCCCeEEEecCCccc-HHHHH
Q 042576 39 KLILAG-TI---QFASAIRAAKPELEKQGFKVMIPQSKPLSA-G--EVLGCTAPKIPARESDFNLVFIADGRFH-LEAFM 110 (313)
Q Consensus 39 ~i~Lv~-ti---Qf~~~l~~~~~~L~~~g~~v~ipq~~pls~-G--evLGCt~~~~~~~~~~d~iv~igdGrFH-le~~m 110 (313)
.|+|+. ++ -|...++.+.+.+++.|+++++-....-.+ . +.+. .+.. ..+|++++.+.-... ...+.
T Consensus 65 ~Igvv~~~~~~~~~~~~~~gi~~~a~~~g~~~~i~~~~~~~~~~~~~~l~----~l~~-~~vdGiii~~~~~~~~~~~~~ 139 (342)
T PRK09526 65 TIGLATTSLALHAPSQIAAAIKSRADQLGYSVVISMVERSGVEACQAAVN----ELLA-QRVSGVIINVPLEDADAEKIV 139 (342)
T ss_pred eEEEEeCCCCcccHHHHHHHHHHHHHHCCCEEEEEeCCCChHHHHHHHHH----HHHh-cCCCEEEEecCCCcchHHHHH
Confidence 477664 22 345567788888999999976521110000 0 1110 0001 237888875321111 22222
Q ss_pred hhCCCceEEEeCCCC-CcccccccChHHHH-HHHHHHHHHHhhcCCEEEEEEeCCCCCCcHHHHHHHHHHHHHcCCcEEE
Q 042576 111 ISNPGIKTFRYDPYL-GKLFLEEYDNKGMR-ETRKRAIEKAMKEARTWGIVLGTLGRQGNPRILERLQKRMEKKGFDYVV 188 (313)
Q Consensus 111 i~np~~~~y~yDPys-~~~~~e~~d~~~~l-~~R~~~I~kak~~A~~~GIIvgTLg~Q~~~~ii~~l~~ll~~~Gkk~y~ 188 (313)
-.....|++.+|-.. ..+.....|....- ..=.++++ + ..+++++|.|..+......-.+-.++-++++|.+...
T Consensus 140 ~~~~~iPvV~~d~~~~~~~~~V~~d~~~~~~~a~~~L~~--~-G~~~I~~l~g~~~~~~~~~R~~Gf~~al~~~gi~~~~ 216 (342)
T PRK09526 140 ADCADVPCLFLDVSPQSPVNSVSFDPEDGTRLGVEHLVE--L-GHQRIALLAGPESSVSARLRLAGWLEYLTDYQLQPIA 216 (342)
T ss_pred hhcCCCCEEEEeccCCCCCCEEEECcHHHHHHHHHHHHH--C-CCCeEEEEeCCCccccHHHHHHHHHHHHHHcCCCcce
Confidence 122357887777421 11222223332211 10011222 3 6689999988766544444555677788888987544
Q ss_pred EEeCCCCH
Q 042576 189 IMMSEISP 196 (313)
Q Consensus 189 i~v~einp 196 (313)
+..+..+.
T Consensus 217 ~~~~~~~~ 224 (342)
T PRK09526 217 VREGDWSA 224 (342)
T ss_pred EEeCCCch
Confidence 44455443
No 85
>cd06286 PBP1_CcpB_like Ligand-binding domain of a novel transcription factor implicated in catabolite repression in Bacillus and Clostridium species. This group includes the ligand-binding domain of a novel transcription factor implicated in catabolite repression in Bacillus and Clostridium species. CcpB is 30% identical in sequence to CcpA which functions as the major transcriptional regulator of carbon catabolite repression/regulation (CCR), a process in which enzymes necessary for the metabolism of alternative sugars are inhibited in the presence of glucose. Like CcpA, the DNA-binding protein CcpB exerts its catabolite-repressing effect by a mechanism dependent on the presence of HPr(Ser-P), the small phosphocarrier proteins of the phosphoenolpyruvate-sugar phosphotransferase system, but with a less significant degree.
Probab=51.73 E-value=60 Score=28.75 Aligned_cols=60 Identities=20% Similarity=0.334 Sum_probs=44.8
Q ss_pred EEEEEEeCCCCCCcHHHHHHHHHHHHHcCCcEEEEEeCCCCHHHHh----cC-cCCccEEEEecCC
Q 042576 155 TWGIVLGTLGRQGNPRILERLQKRMEKKGFDYVVIMMSEISPARVA----LF-EDSVDAWIQIACP 215 (313)
Q Consensus 155 ~~GIIvgTLg~Q~~~~ii~~l~~ll~~~Gkk~y~i~v~einp~KLa----nf-~~~ID~fV~iaCP 215 (313)
++|+|+..+.......+++.+++.+++.|....+. .+.-++++.. .+ ...+|++|+.+|.
T Consensus 1 ~i~~i~~~~~~~~~~~i~~gi~~~~~~~g~~~~~~-~~~~~~~~~~~~i~~l~~~~vdgiii~~~~ 65 (260)
T cd06286 1 TIGVVLPYINHPYFSQLVDGIEKAALKHGYKVVLL-QTNYDKEKELEYLELLKTKQVDGLILCSRE 65 (260)
T ss_pred CEEEEeCCCCCchHHHHHHHHHHHHHHcCCEEEEE-eCCCChHHHHHHHHHHHHcCCCEEEEeCCC
Confidence 48999998888889999999999999999877554 4455665432 12 1149999998774
No 86
>cd06284 PBP1_LacI_like_6 Ligand-binding domain of an uncharacterized transcription regulator from Actinobacillus succinogenes and its close homologs from other bacteria. This group includes the ligand-binding domain of an uncharacterized transcription regulator from Actinobacillus succinogenes and its close homologs from other bacteria. This group belongs to the the LacI-GalR family repressors and are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding.
Probab=51.58 E-value=56 Score=28.85 Aligned_cols=58 Identities=12% Similarity=0.210 Sum_probs=32.1
Q ss_pred EEEEEeCCCCCCcHHHHHHHHHHHHHcCCcEEEEEeCCCCHHHHhcC-----cCCccEEEEecC
Q 042576 156 WGIVLGTLGRQGNPRILERLQKRMEKKGFDYVVIMMSEISPARVALF-----EDSVDAWIQIAC 214 (313)
Q Consensus 156 ~GIIvgTLg~Q~~~~ii~~l~~ll~~~Gkk~y~i~v~einp~KLanf-----~~~ID~fV~iaC 214 (313)
||+|+.+++-..+..+.+.+++.++++|....++. +.-++++.... ...+|++++.++
T Consensus 2 i~~v~~~~~~~~~~~~~~~i~~~~~~~g~~~~~~~-~~~~~~~~~~~~~~~~~~~vdgiii~~~ 64 (267)
T cd06284 2 ILVLVPDIANPFFSEILKGIEDEAREAGYGVLLGD-TRSDPEREQEYLDLLRRKQADGIILLDG 64 (267)
T ss_pred EEEEECCCCCccHHHHHHHHHHHHHHcCCeEEEec-CCCChHHHHHHHHHHHHcCCCEEEEecC
Confidence 56666666666666677777777777666554333 33344332211 113666666554
No 87
>cd06294 PBP1_ycjW_transcription_regulator_like Ligand-binding domain of uncharacterized transcription regulator ycjW which is a member of the LacI-GalR family repressors. This group includes the ligand-binding domain of uncharacterized transcription regulator ycjW which is a member of the LacI-GalR family repressors that are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.
Probab=51.50 E-value=1.7e+02 Score=25.79 Aligned_cols=131 Identities=12% Similarity=0.142 Sum_probs=62.2
Q ss_pred ccHhHHHHHHHHHHhCCCeEEecCCCCCCCccccCCCCCC-CCCCCCCCeEEEecCCcc-cHHHHHhhCCCceEEEeCCC
Q 042576 47 QFASAIRAAKPELEKQGFKVMIPQSKPLSAGEVLGCTAPK-IPARESDFNLVFIADGRF-HLEAFMISNPGIKTFRYDPY 124 (313)
Q Consensus 47 Qf~~~l~~~~~~L~~~g~~v~ipq~~pls~GevLGCt~~~-~~~~~~~d~iv~igdGrF-Hle~~mi~np~~~~y~yDPy 124 (313)
-|...++.+.+.+++.|+++.+..... +.+-.. .... +.. ..+|+++..+.... ..... +..-++|++.+|..
T Consensus 18 ~~~~~~~~~~~~~~~~g~~~~~~~~~~--~~~~~~-~~~~~~~~-~~~dgiii~~~~~~~~~~~~-~~~~~ipvV~~~~~ 92 (270)
T cd06294 18 FFIEVLRGISAVANENGYDISLATGKN--EEELLE-EVKKMIQQ-KRVDGFILLYSREDDPIIDY-LKEEKFPFVVIGKP 92 (270)
T ss_pred CHHHHHHHHHHHHHHCCCEEEEecCCC--cHHHHH-HHHHHHHH-cCcCEEEEecCcCCcHHHHH-HHhcCCCEEEECCC
Confidence 345556778888888888876521110 000000 0000 000 13688877653211 22122 23346788888854
Q ss_pred CCc---ccccccChHHHHHHHHHHHHHHhhcCCEEEEEEeCCCCCCcHHHHHHHHHHHHHcCC
Q 042576 125 LGK---LFLEEYDNKGMRETRKRAIEKAMKEARTWGIVLGTLGRQGNPRILERLQKRMEKKGF 184 (313)
Q Consensus 125 s~~---~~~e~~d~~~~l~~R~~~I~kak~~A~~~GIIvgTLg~Q~~~~ii~~l~~ll~~~Gk 184 (313)
... +.....|..+. -|..+=.-++...+++++|-|..+......-.+-.++.++++|.
T Consensus 93 ~~~~~~~~~v~~d~~~~--g~~~~~~l~~~g~~~i~~i~~~~~~~~~~~r~~gf~~~~~~~~~ 153 (270)
T cd06294 93 EDDKENITYVDNDNIQA--GYDATEYLIKLGHKKIAFVGGDLDLEVTQDRLQGYKQALEDHGI 153 (270)
T ss_pred CCCCCCCCeEEECcHHH--HHHHHHHHHHcCCccEEEecCCcccHHHHHHHHHHHHHHHHcCC
Confidence 321 22122333222 12111111111557899997665544333445566778888874
No 88
>TIGR01162 purE phosphoribosylaminoimidazole carboxylase, PurE protein. Phosphoribosylaminoimidazole carboxylase is a fusion protein in plants and fungi, but consists of two non-interacting proteins in bacteria, PurK and PurE. This model represents PurK, an N5-CAIR mutase.
Probab=51.41 E-value=46 Score=29.35 Aligned_cols=55 Identities=18% Similarity=0.355 Sum_probs=42.5
Q ss_pred EEEEEeCCCCCCcHHHHHHHHHHHHHcCCcEEEEEeC-CCCHHHHhcCc-----CCccEEEEec
Q 042576 156 WGIVLGTLGRQGNPRILERLQKRMEKKGFDYVVIMMS-EISPARVALFE-----DSVDAWIQIA 213 (313)
Q Consensus 156 ~GIIvgTLg~Q~~~~ii~~l~~ll~~~Gkk~y~i~v~-einp~KLanf~-----~~ID~fV~ia 213 (313)
+|||+|+ .-...+++...+.|++-|..+-+-+.| .=+|++|..|- .++++||-+|
T Consensus 1 V~IimGS---~SD~~~~~~a~~~L~~~gi~~dv~V~SaHRtp~~~~~~~~~a~~~g~~viIa~A 61 (156)
T TIGR01162 1 VGIIMGS---DSDLPTMKKAADILEEFGIPYELRVVSAHRTPELMLEYAKEAEERGIKVIIAGA 61 (156)
T ss_pred CEEEECc---HhhHHHHHHHHHHHHHcCCCeEEEEECcccCHHHHHHHHHHHHHCCCeEEEEeC
Confidence 4788877 667889999999999999998766666 67889988883 1478887544
No 89
>cd06267 PBP1_LacI_sugar_binding_like Ligand binding domain of the LacI tanscriptional regulator family belonging to the type I periplasmic-binding fold protein superfamily. Ligand binding domain of the LacI tanscriptional regulator family belonging to the type I periplasmic-binding fold protein superfamily. In most cases, ligands are monosaccharide including lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars. The LacI family of proteins consists of transcriptional regulators related to the lac repressor. In this case, the domain sugar binding changes the DNA binding activity of the repressor domain.
Probab=51.38 E-value=1.6e+02 Score=25.45 Aligned_cols=34 Identities=18% Similarity=0.220 Sum_probs=24.6
Q ss_pred cCCEEEEEEeCCCCCCcHHHHHHHHHHHHHcCCc
Q 042576 152 EARTWGIVLGTLGRQGNPRILERLQKRMEKKGFD 185 (313)
Q Consensus 152 ~A~~~GIIvgTLg~Q~~~~ii~~l~~ll~~~Gkk 185 (313)
..+++++|.+..+-.....-.+-+++.+++.|.+
T Consensus 115 g~~~i~~i~~~~~~~~~~~r~~g~~~~~~~~~~~ 148 (264)
T cd06267 115 GHRRIAFIGGPPDLSTARERLEGYREALEEAGIP 148 (264)
T ss_pred CCceEEEecCCCccchHHHHHHHHHHHHHHcCCC
Confidence 4678999988766455555667778888888843
No 90
>cd06275 PBP1_PurR Ligand-binding domain of purine repressor, PurR, which functions as the master regulatory protein of de novo purine nucleotide biosynthesis in Escherichia coli. Ligand-binding domain of purine repressor, PurR, which functions as the master regulatory protein of de novo purine nucleotide biosynthesis in Escherichia coli. This dimeric PurR belongs to the LacI-GalR family of transcription regulators and is activated to bind to DNA operator sites by initially binding either of high affinity corepressors, hypoxanthine or guanine. PurR is composed of two functional domains: aan N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the purine transcription repressor undergoes a
Probab=51.23 E-value=61 Score=28.81 Aligned_cols=60 Identities=15% Similarity=0.312 Sum_probs=37.3
Q ss_pred EEEEEEeCCCCCCcHHHHHHHHHHHHHcCCcEEEEEeCCCCHHHHh----cCc-CCccEEEEecCC
Q 042576 155 TWGIVLGTLGRQGNPRILERLQKRMEKKGFDYVVIMMSEISPARVA----LFE-DSVDAWIQIACP 215 (313)
Q Consensus 155 ~~GIIvgTLg~Q~~~~ii~~l~~ll~~~Gkk~y~i~v~einp~KLa----nf~-~~ID~fV~iaCP 215 (313)
+||+|+.+.....+..+++.+++.+++.|....++ .++=++++.. .+. ..+|++|+.++-
T Consensus 1 ~igvi~~~~~~~~~~~~~~gi~~~~~~~g~~~~~~-~~~~~~~~~~~~i~~l~~~~vdgiii~~~~ 65 (269)
T cd06275 1 TIGMLVTTSTNPFFAEVVRGVEQYCYRQGYNLILC-NTEGDPERQRSYLRMLAQKRVDGLLVMCSE 65 (269)
T ss_pred CEEEEeCCCCcchHHHHHHHHHHHHHHcCCEEEEE-eCCCChHHHHHHHHHHHHcCCCEEEEecCC
Confidence 37888877766677778888888888887665433 2333454322 221 137888877653
No 91
>cd06296 PBP1_CatR_like Ligand-binding domain of a LacI-like transcriptional regulator, CatR which is involved in catechol degradation. This group includes the ligand-binding domain of a LacI-like transcriptional regulator, CatR which is involved in catechol degradation. This group belongs to the the LacI-GalR family repressors that are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.
Probab=50.92 E-value=54 Score=29.14 Aligned_cols=34 Identities=21% Similarity=0.387 Sum_probs=23.3
Q ss_pred EEEEEeCCCCCCcHHHHHHHHHHHHHcCCcEEEE
Q 042576 156 WGIVLGTLGRQGNPRILERLQKRMEKKGFDYVVI 189 (313)
Q Consensus 156 ~GIIvgTLg~Q~~~~ii~~l~~ll~~~Gkk~y~i 189 (313)
+|||+.++.......+++.+++.+++.|.+..++
T Consensus 2 i~vi~~~~~~~~~~~~~~gi~~~~~~~g~~~~~~ 35 (270)
T cd06296 2 IGLVFPDLDSPWASEVLRGVEEAAAAAGYDVVLS 35 (270)
T ss_pred eEEEECCCCCccHHHHHHHHHHHHHHcCCeEEEe
Confidence 6777777666777777777777777777655433
No 92
>cd06282 PBP1_GntR_like_2 Ligand-binding domain of putative DNA transcription repressors highly similar to that of the repressor specific for gluconate (GntR) which is a member of the LacI-GalR family of bacterial transcription regulators. This group includes the ligand-binding domain of putative DNA transcription repressors highly similar to that of the repressor specific for gluconate (GntR) which is a member of the LacI-GalR family of bacterial transcription regulators. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding
Probab=50.62 E-value=41 Score=29.72 Aligned_cols=32 Identities=19% Similarity=0.363 Sum_probs=15.1
Q ss_pred EEEEEeCCCCCCcHHHHHHHHHHHHHcCCcEE
Q 042576 156 WGIVLGTLGRQGNPRILERLQKRMEKKGFDYV 187 (313)
Q Consensus 156 ~GIIvgTLg~Q~~~~ii~~l~~ll~~~Gkk~y 187 (313)
||+|+...+.-.+..+++.+++.+++.|....
T Consensus 2 igvv~~~~~~~~~~~~~~~i~~~~~~~g~~~~ 33 (266)
T cd06282 2 VGVVLPSLANPVFAECVQGIQEEARAAGYSLL 33 (266)
T ss_pred eEEEeCCCCcchHHHHHHHHHHHHHHCCCEEE
Confidence 45555444433444455555555555444433
No 93
>cd06290 PBP1_LacI_like_9 Ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. This group includes the ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.
Probab=50.47 E-value=44 Score=29.74 Aligned_cols=60 Identities=20% Similarity=0.343 Sum_probs=37.3
Q ss_pred EEEEEEeCCCCCCcHHHHHHHHHHHHHcCCcEEEEEeCCCCHHHHh----cCc-CCccEEEEecCC
Q 042576 155 TWGIVLGTLGRQGNPRILERLQKRMEKKGFDYVVIMMSEISPARVA----LFE-DSVDAWIQIACP 215 (313)
Q Consensus 155 ~~GIIvgTLg~Q~~~~ii~~l~~ll~~~Gkk~y~i~v~einp~KLa----nf~-~~ID~fV~iaCP 215 (313)
+||+|+..+.-.....+++.+++.+++.|....++ .+.-++++.. ++. ..+|.+++.+|.
T Consensus 1 ~i~vi~~~~~~~~~~~~~~gi~~~~~~~gy~~~~~-~~~~~~~~~~~~i~~l~~~~~dgiii~~~~ 65 (265)
T cd06290 1 TIGVLTQDFASPFYGRILKGMERGLNGSGYSPIIA-TGHWNQSRELEALELLKSRRVDALILLGGD 65 (265)
T ss_pred CEEEEECCCCCchHHHHHHHHHHHHHHCCCEEEEE-eCCCCHHHHHHHHHHHHHCCCCEEEEeCCC
Confidence 36788877766667777888888888877665443 3445554332 221 137888877663
No 94
>PRK10653 D-ribose transporter subunit RbsB; Provisional
Probab=50.40 E-value=41 Score=30.93 Aligned_cols=62 Identities=19% Similarity=0.215 Sum_probs=44.0
Q ss_pred cCCEEEEEEeCCCCCCcHHHHHHHHHHHHHcCCcEEEEEeCCCCHHHHh----cCc-CCccEEEEecC
Q 042576 152 EARTWGIVLGTLGRQGNPRILERLQKRMEKKGFDYVVIMMSEISPARVA----LFE-DSVDAWIQIAC 214 (313)
Q Consensus 152 ~A~~~GIIvgTLg~Q~~~~ii~~l~~ll~~~Gkk~y~i~v~einp~KLa----nf~-~~ID~fV~iaC 214 (313)
+.+++|+|+.++.--.+..+++.+++.++++|....++.. .-++++.. ++. ..+|+.|+.+.
T Consensus 25 ~~~~I~vi~~~~~~~f~~~~~~~i~~~~~~~G~~~~~~~~-~~d~~~~~~~~~~l~~~~~dgiii~~~ 91 (295)
T PRK10653 25 AKDTIALVVSTLNNPFFVSLKDGAQKEADKLGYNLVVLDS-QNNPAKELANVQDLTVRGTKILLINPT 91 (295)
T ss_pred cCCeEEEEecCCCChHHHHHHHHHHHHHHHcCCeEEEecC-CCCHHHHHHHHHHHHHcCCCEEEEcCC
Confidence 5789999999888777889999999999999977765433 23444332 221 14888887654
No 95
>cd01538 PBP1_ABC_xylose_binding Periplasmic xylose-binding component of the ABC-type transport systems that belong to a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein (PBP1) superfamily. Periplasmic xylose-binding component of the ABC-type transport systems that belong to a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein (PBP1) superfamily, which consists of two alpha/beta globular domains connected by a three-stranded hinge. This Venus flytrap-like domain undergoes a transition from an open to a closed conformational state upon ligand binding. Moreover, the periplasmic xylose-binding protein is homologous to the ligand-binding domain of eukaryotic receptors such as glutamate receptor (GluR) and DNA-binding transcriptional repressors such as LacI and GalR.
Probab=50.33 E-value=27 Score=31.99 Aligned_cols=30 Identities=17% Similarity=0.163 Sum_probs=13.1
Q ss_pred EEEEEeCCCCCCcHHHHHHHHHHHHHcCCc
Q 042576 156 WGIVLGTLGRQGNPRILERLQKRMEKKGFD 185 (313)
Q Consensus 156 ~GIIvgTLg~Q~~~~ii~~l~~ll~~~Gkk 185 (313)
||+|+..+.-.....+++.+++.+++.|..
T Consensus 2 I~vi~~~~~~~~~~~~~~gi~~~a~~~g~~ 31 (288)
T cd01538 2 IGLSLPTKTEERWIRDRPNFEAALKELGAE 31 (288)
T ss_pred eEEEEeCCCcHHHHHHHHHHHHHHHHcCCE
Confidence 444444433333334444444444444443
No 96
>cd06284 PBP1_LacI_like_6 Ligand-binding domain of an uncharacterized transcription regulator from Actinobacillus succinogenes and its close homologs from other bacteria. This group includes the ligand-binding domain of an uncharacterized transcription regulator from Actinobacillus succinogenes and its close homologs from other bacteria. This group belongs to the the LacI-GalR family repressors and are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding.
Probab=49.99 E-value=1.8e+02 Score=25.55 Aligned_cols=45 Identities=16% Similarity=0.189 Sum_probs=26.2
Q ss_pred cCCEEEEEEeCCCCCCcHHHHHHHHHHHHHcCCc--EEEEEeCCCCH
Q 042576 152 EARTWGIVLGTLGRQGNPRILERLQKRMEKKGFD--YVVIMMSEISP 196 (313)
Q Consensus 152 ~A~~~GIIvgTLg~Q~~~~ii~~l~~ll~~~Gkk--~y~i~v~einp 196 (313)
..++++++-+...-.....-.+-.++.++++|.+ ...+..+..++
T Consensus 114 g~~~i~~l~~~~~~~~~~~r~~gf~~~~~~~~~~~~~~~~~~~~~~~ 160 (267)
T cd06284 114 GHRRIALITGPRDNPLARDRLEGYRQALAEAGLPADEELIQEGDFSL 160 (267)
T ss_pred CCceEEEEcCCccchhHHHHHHHHHHHHHHcCCCCCcceEEeCCCCh
Confidence 4568988876544333344455666778888843 22344455554
No 97
>COG0716 FldA Flavodoxins [Energy production and conversion]
Probab=48.94 E-value=64 Score=27.32 Aligned_cols=59 Identities=15% Similarity=0.116 Sum_probs=41.9
Q ss_pred CEEEEEEeCCCCCCcHHHHHHHHHHHHHcCCcEEEEEeCCCCHHHHhcCcCCccEEEEecCCCc
Q 042576 154 RTWGIVLGTLGRQGNPRILERLQKRMEKKGFDYVVIMMSEISPARVALFEDSVDAWIQIACPRL 217 (313)
Q Consensus 154 ~~~GIIvgTLg~Q~~~~ii~~l~~ll~~~Gkk~y~i~v~einp~KLanf~~~ID~fV~iaCPrl 217 (313)
.+++|+.||.. -+...|+++|++.|.+.|.+..+.....+....+ + +.|.++..+.+-.
T Consensus 2 ~ki~Ivy~S~t-GnTe~vA~~i~~~l~~~~~~~~~~~~~~~~~~~~--~--~~d~~~~g~~t~~ 60 (151)
T COG0716 2 MKILIVYGSRT-GNTEKVAEIIAEELGADGFEVDIDIRPGIKDDLL--E--SYDELLLGTPTWG 60 (151)
T ss_pred CeEEEEEEcCC-CcHHHHHHHHHHHhccCCceEEEeecCCcchhhh--c--cCCEEEEEeCCCC
Confidence 46899999987 3455699999999999998884444444444333 3 3678888877764
No 98
>cd06292 PBP1_LacI_like_10 Ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. This group includes the ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.
Probab=48.86 E-value=44 Score=29.87 Aligned_cols=59 Identities=14% Similarity=0.162 Sum_probs=38.8
Q ss_pred EEEEEEeCCCCCCcHHHHHHHHHHHHHcCCcEEEEEeCCCCHHHHh----cCc-CCccEEEEecC
Q 042576 155 TWGIVLGTLGRQGNPRILERLQKRMEKKGFDYVVIMMSEISPARVA----LFE-DSVDAWIQIAC 214 (313)
Q Consensus 155 ~~GIIvgTLg~Q~~~~ii~~l~~ll~~~Gkk~y~i~v~einp~KLa----nf~-~~ID~fV~iaC 214 (313)
.||+|+..+..-.+..+++.+++.+++.|....++ -+.-++++-. ++. ..+|..+++++
T Consensus 1 ~Igvi~~~~~~~~~~~~~~gi~~~~~~~g~~~~~~-~~~~~~~~~~~~i~~l~~~~vdgiIi~~~ 64 (273)
T cd06292 1 LVGLLVPELSNPIFPAFAEAIEAALAQYGYTVLLC-NTYRGGVSEADYVEDLLARGVRGVVFISS 64 (273)
T ss_pred CEEEEeCCCcCchHHHHHHHHHHHHHHCCCEEEEE-eCCCChHHHHHHHHHHHHcCCCEEEEeCC
Confidence 37888888877778888888888888888765433 3333443222 221 14888888654
No 99
>cd06302 PBP1_LsrB_Quorum_Sensing Periplasmic binding domain of autoinducer-2 (AI-2) receptor LsrB from Salmonella typhimurium and its close homologs. Periplasmic binding domain of autoinducer-2 (AI-2) receptor LsrB from Salmonella typhimurium and its close homologs from other bacteria. The members of this group are homologous to a family of periplasmic pentose/hexose sugar-binding proteins that function as the primary receptors for chemotaxis and transporters of many sugar based solutes in bacteria and archaea and that are a member of the type I periplasmic binding protein superfamily. LsrB binds a chemically distinct form of the AI-2 signal that lacks boron, in contrast to the Vibrio harveyi AI-2 signaling molecule that has an unusual furanosyl borate diester. Hence, many bacteria coordinate their gene expression according to the local density of their population by producing species specific AI-2. This process of quorum sensing allows LsrB to function as a periplasmic AI-2 binding p
Probab=48.28 E-value=44 Score=30.90 Aligned_cols=59 Identities=19% Similarity=0.134 Sum_probs=35.2
Q ss_pred EEEEEEeCCCCCCcHHHHHHHHHHHHHcCCcEEEEEeCCCCHHHHh----cC-cCCccEEEEec
Q 042576 155 TWGIVLGTLGRQGNPRILERLQKRMEKKGFDYVVIMMSEISPARVA----LF-EDSVDAWIQIA 213 (313)
Q Consensus 155 ~~GIIvgTLg~Q~~~~ii~~l~~ll~~~Gkk~y~i~v~einp~KLa----nf-~~~ID~fV~ia 213 (313)
+||+|+.+..-.....+++.+++.+++.|.+..++.-+.-++++-. ++ ...+|+.|+.+
T Consensus 1 ~I~vi~~~~~~~f~~~i~~gi~~~a~~~g~~v~~~~~~~~d~~~~~~~i~~~~~~~~DgiIi~~ 64 (298)
T cd06302 1 TIAFVPKVTGIPYFNRMEEGAKEAAKELGVDAIYVGPTTADAAGQVQIIEDLIAQGVDAIAVVP 64 (298)
T ss_pred CEEEEEcCCCChHHHHHHHHHHHHHHHhCCeEEEECCCCCCHHHHHHHHHHHHhcCCCEEEEec
Confidence 4677777766666777777777777777766554433444444322 22 11377777764
No 100
>PRK05282 (alpha)-aspartyl dipeptidase; Validated
Probab=48.17 E-value=65 Score=29.99 Aligned_cols=45 Identities=11% Similarity=0.110 Sum_probs=34.3
Q ss_pred hHHHHHHHHHhCCCCCeEEEEeccc----cHhHHHHHHHHHHhCCCeEE
Q 042576 23 VNRLIDTIKVNYSDPGKLILAGTIQ----FASAIRAAKPELEKQGFKVM 67 (313)
Q Consensus 23 ~~~~i~~i~~~f~~~~~i~Lv~tiQ----f~~~l~~~~~~L~~~g~~v~ 67 (313)
++|..+.+..-+...++|+++-|.. +...++..++.+++.|.++.
T Consensus 17 l~~~~~~~~~~~~~~~~v~fIPtAs~~~~~~~y~~~~~~af~~lG~~v~ 65 (233)
T PRK05282 17 LEHALPLIAELLAGRRKAVFIPYAGVTQSWDDYTAKVAEALAPLGIEVT 65 (233)
T ss_pred HHHHHHHHHHHHcCCCeEEEECCCCCCCCHHHHHHHHHHHHHHCCCEEE
Confidence 5787778777666567899998776 55667888889998888854
No 101
>cd06278 PBP1_LacI_like_2 Ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. This group includes the ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.
Probab=48.15 E-value=62 Score=28.55 Aligned_cols=34 Identities=24% Similarity=0.511 Sum_probs=20.0
Q ss_pred EEEEEeCCCCCCcHHHHHHHHHHHHHcCCcEEEE
Q 042576 156 WGIVLGTLGRQGNPRILERLQKRMEKKGFDYVVI 189 (313)
Q Consensus 156 ~GIIvgTLg~Q~~~~ii~~l~~ll~~~Gkk~y~i 189 (313)
||+|+....-.....+++.+++.+++.|.+..++
T Consensus 2 I~~i~~~~~~~~~~~~~~~i~~~~~~~g~~~~~~ 35 (266)
T cd06278 2 IGVVVADLDNPFYSELLEALSRALQARGYQPLLI 35 (266)
T ss_pred EEEEeCCCCCchHHHHHHHHHHHHHHCCCeEEEE
Confidence 5666655554555556666666666666554433
No 102
>cd06325 PBP1_ABC_uncharacterized_transporter Type I periplasmic ligand-binding domain of uncharacterized ABC-type transport systems that are predicted to be involved in the uptake of amino acids, peptides, or inorganic ions. This group includes the type I periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type transport systems that are predicted to be involved in the uptake of amino acids, peptides, or inorganic ions. This subgroup has high sequence similarity to members of the family of hydrophobic amino acid transporters (HAAT), such as leucine/isoleucine/valine binding protein (LIVBP); its ligand specificity has not been determined experimentally.
Probab=47.94 E-value=1.7e+02 Score=26.08 Aligned_cols=36 Identities=22% Similarity=0.324 Sum_probs=25.1
Q ss_pred cCCEEEEEEeCCCCCCcHHHHHHHHHHHHHcCCcEEE
Q 042576 152 EARTWGIVLGTLGRQGNPRILERLQKRMEKKGFDYVV 188 (313)
Q Consensus 152 ~A~~~GIIvgTLg~Q~~~~ii~~l~~ll~~~Gkk~y~ 188 (313)
..+++|+|.++.. .......+.+++.+++.|.+...
T Consensus 130 g~~~i~~l~~~~~-~~~~~r~~g~~~~~~~~g~~~~~ 165 (281)
T cd06325 130 DAKTVGVLYNPSE-ANSVVQVKELKKAAAKLGIEVVE 165 (281)
T ss_pred CCcEEEEEeCCCC-ccHHHHHHHHHHHHHhCCCEEEE
Confidence 6789999977654 23345567788888888876443
No 103
>cd01452 VWA_26S_proteasome_subunit 26S proteasome plays a major role in eukaryotic protein breakdown, especially for ubiquitin-tagged proteins. It is an ATP-dependent protease responsible for the bulk of non-lysosomal proteolysis in eukaryotes, often using covalent modification of proteins by ubiquitylation. It consists of a 20S proteolytic core particle (CP) and a 19S regulatory particle (RP). The CP is an ATP independent peptidase consisting of hydrolyzing activities. One or both ends of CP carry the RP that confers both ubiquitin and ATP dependence to the 26S proteosome. The RP's proposed functions include recognition of substrates and translocation of these to CP for proteolysis. The RP can dissociate into a stable lid and base subcomplexes. The base is composed of three non-ATPase subunits (Rpn 1, 2 and 10). A single residue in the vWA domain of Rpn10 has been implicated to be responsible for stabilizing the lid-base association.
Probab=47.02 E-value=60 Score=29.23 Aligned_cols=49 Identities=20% Similarity=0.314 Sum_probs=38.2
Q ss_pred CEEEEEEeCCCCCCcHHHHHHHHHHHHHcCCcEEEEEeCCC--CHHHHhcCc
Q 042576 154 RTWGIVLGTLGRQGNPRILERLQKRMEKKGFDYVVIMMSEI--SPARVALFE 203 (313)
Q Consensus 154 ~~~GIIvgTLg~Q~~~~ii~~l~~ll~~~Gkk~y~i~v~ei--np~KLanf~ 203 (313)
+++-|++|+.+--.-.. +..+-+.|++.|.+.+++.+|+. |.+||..|-
T Consensus 108 ~rivi~v~S~~~~d~~~-i~~~~~~lkk~~I~v~vI~~G~~~~~~~~l~~~~ 158 (187)
T cd01452 108 QRIVAFVGSPIEEDEKD-LVKLAKRLKKNNVSVDIINFGEIDDNTEKLTAFI 158 (187)
T ss_pred ceEEEEEecCCcCCHHH-HHHHHHHHHHcCCeEEEEEeCCCCCCHHHHHHHH
Confidence 47889999987654444 44566677889999999999954 688999885
No 104
>COG1832 Predicted CoA-binding protein [General function prediction only]
Probab=46.78 E-value=28 Score=30.19 Aligned_cols=95 Identities=15% Similarity=0.145 Sum_probs=51.9
Q ss_pred HHHHhCCCCCeEEEEec-cccHhHHHHHHHHHHhCCCeEEecCCCCCCCccccCCC-CCCCCCC-CCCCeEEEecCCccc
Q 042576 29 TIKVNYSDPGKLILAGT-IQFASAIRAAKPELEKQGFKVMIPQSKPLSAGEVLGCT-APKIPAR-ESDFNLVFIADGRFH 105 (313)
Q Consensus 29 ~i~~~f~~~~~i~Lv~t-iQf~~~l~~~~~~L~~~g~~v~ipq~~pls~GevLGCt-~~~~~~~-~~~d~iv~igdGrFH 105 (313)
.++..+.+.++||+|+- -.=...-..+.+.|.++||+|+ |-+-.+.-+||||=- ++++.+. ..+|.+-+.-.+.+-
T Consensus 8 ~i~~iL~~~K~IAvVG~S~~P~r~sy~V~kyL~~~GY~Vi-PVNP~~~~~eiLG~k~y~sL~dIpe~IDiVdvFR~~e~~ 86 (140)
T COG1832 8 DIAEILKSAKTIAVVGASDKPDRPSYRVAKYLQQKGYRVI-PVNPKLAGEEILGEKVYPSLADIPEPIDIVDVFRRSEAA 86 (140)
T ss_pred HHHHHHHhCceEEEEecCCCCCccHHHHHHHHHHCCCEEE-eeCcccchHHhcCchhhhcHHhCCCCCcEEEEecChhhh
Confidence 34444555678999973 2223335668889999999965 333223446899953 4444321 247777554444433
Q ss_pred HH----HHHhhCCCceEEEeCCCC
Q 042576 106 LE----AFMISNPGIKTFRYDPYL 125 (313)
Q Consensus 106 le----~~mi~np~~~~y~yDPys 125 (313)
++ .+.+. +..=|++..-.+
T Consensus 87 ~~i~~eal~~~-~kv~W~QlGi~n 109 (140)
T COG1832 87 PEVAREALEKG-AKVVWLQLGIRN 109 (140)
T ss_pred HHHHHHHHhhC-CCeEEEecCcCC
Confidence 22 22222 334455655443
No 105
>TIGR03705 poly_P_kin polyphosphate kinase 1. Members of this protein family are the enzyme polyphosphate kinase 1 (PPK1). This family is found in many prokaryotes and also in Dictyostelium. Sequences in the seed alignment were taken from prokaryotic consecutive two-gene pairs in which the other gene encodes an exopolyphosphatase. It synthesizes polyphosphate from the terminal phosphate of ATP but not GTP, in contrast to PPK2.
Probab=46.30 E-value=4.2e+02 Score=28.73 Aligned_cols=92 Identities=20% Similarity=0.340 Sum_probs=53.1
Q ss_pred eEEEecCCcccHHHHHhhCCCceEEEeCCC---------------C-----CcccccccC-hHHHHHHHHHHHHHHhhcC
Q 042576 95 NLVFIADGRFHLEAFMISNPGIKTFRYDPY---------------L-----GKLFLEEYD-NKGMRETRKRAIEKAMKEA 153 (313)
Q Consensus 95 ~iv~igdGrFHle~~mi~np~~~~y~yDPy---------------s-----~~~~~e~~d-~~~~l~~R~~~I~kak~~A 153 (313)
...++|.|.|+...+.+. .+..++..|+. + +.+.....+ .++++..=...|+.|+ ..
T Consensus 442 ~y~~igTgN~n~~ta~~y-~D~~l~t~~~~i~~d~~~~F~~l~~~~~~~~~~~l~~~P~~~~~~~~~~i~~ei~~Ak-~g 519 (672)
T TIGR03705 442 RYVHLGTGNYHPKTARLY-TDLSLFTADPEIGRDVARVFNYLTGYSRPPKFKHLLVSPFTLRKRLLELIDREIENAR-AG 519 (672)
T ss_pred EEEEecCCCCCCcccccc-cceeEEEeChHHHHHHHHHHHHhhCCCcchhhHHHHhCcchHHHHHHHHHHHHHHHHH-cC
Confidence 467899999997655543 34445544441 1 111111111 1222322234667777 65
Q ss_pred CEEEEEEeCCCCCCcHHHHHHHHHHHHHcCCcEEEEE
Q 042576 154 RTWGIVLGTLGRQGNPRILERLQKRMEKKGFDYVVIM 190 (313)
Q Consensus 154 ~~~GIIvgTLg~Q~~~~ii~~l~~ll~~~Gkk~y~i~ 190 (313)
+.=.|++-|-... ...++++|... .++|.++-+++
T Consensus 520 ~~~~I~ik~n~l~-D~~ii~aL~~A-s~aGV~V~Liv 554 (672)
T TIGR03705 520 KPARIIAKMNSLV-DPDLIDALYEA-SQAGVKIDLIV 554 (672)
T ss_pred CCCEEEEEcCCCC-CHHHHHHHHHH-HHCCCeEEEEE
Confidence 5455666666655 78888888765 45799988887
No 106
>PRK09004 FMN-binding protein MioC; Provisional
Probab=46.25 E-value=64 Score=27.47 Aligned_cols=53 Identities=13% Similarity=0.313 Sum_probs=36.6
Q ss_pred CEEEEEEeCCCCCCcHHHHHHHHHHHHHcCCcEEEEEeCCCCHHHHhcCcCCccEEEEec
Q 042576 154 RTWGIVLGTLGRQGNPRILERLQKRMEKKGFDYVVIMMSEISPARVALFEDSVDAWIQIA 213 (313)
Q Consensus 154 ~~~GIIvgTLg~Q~~~~ii~~l~~ll~~~Gkk~y~i~v~einp~KLanf~~~ID~fV~ia 213 (313)
+++.|+.||-++ ....+.++|.+.+++.|.++.++-+. .++. ++ +.|.+|++.
T Consensus 2 ~~i~I~ygS~tG-nae~~A~~l~~~~~~~g~~~~~~~~~--~~~~---l~-~~~~li~~~ 54 (146)
T PRK09004 2 ADITLISGSTLG-GAEYVADHLAEKLEEAGFSTETLHGP--LLDD---LS-ASGLWLIVT 54 (146)
T ss_pred CeEEEEEEcCch-HHHHHHHHHHHHHHHcCCceEEeccC--CHHH---hc-cCCeEEEEE
Confidence 368899999763 34569999999999999988765443 3444 44 355544443
No 107
>cd01575 PBP1_GntR Ligand-binding domain of DNA transcription repressor GntR specific for gluconate, a member of the LacI-GalR family of bacterial transcription regulators. This group represents the ligand-binding domain of DNA transcription repressor GntR specific for gluconate, a member of the LacI-GalR family of bacterial transcription regulators. The ligand-binding domain of GntR is structurally homologous to the periplasmic sugar-binding domain of ABC-type transporters and both domains contain the type I periplasmic binding protein-like fold. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the type I periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding,
Probab=46.25 E-value=56 Score=28.89 Aligned_cols=60 Identities=13% Similarity=0.208 Sum_probs=41.4
Q ss_pred EEEEEEeCCCCCCcHHHHHHHHHHHHHcCCcEEEEEeCCCCHHHHh----cC-cCCccEEEEecCC
Q 042576 155 TWGIVLGTLGRQGNPRILERLQKRMEKKGFDYVVIMMSEISPARVA----LF-EDSVDAWIQIACP 215 (313)
Q Consensus 155 ~~GIIvgTLg~Q~~~~ii~~l~~ll~~~Gkk~y~i~v~einp~KLa----nf-~~~ID~fV~iaCP 215 (313)
+||+|+.......+..+++.+++.+++.|.+..++. +.-++++.. .+ ...+|+.|++++.
T Consensus 1 ~Ig~i~~~~~~~~~~~~~~gi~~~~~~~g~~~~~~~-~~~~~~~~~~~~~~l~~~~vdgiii~~~~ 65 (268)
T cd01575 1 LVAVLVPSLSNSVFADVLQGISDVLEAAGYQLLLGN-TGYSPEREEELLRTLLSRRPAGLILTGLE 65 (268)
T ss_pred CEEEEeCCCcchhHHHHHHHHHHHHHHcCCEEEEec-CCCCchhHHHHHHHHHHcCCCEEEEeCCC
Confidence 478888888777888888889999998887765543 344554432 11 1148888888764
No 108
>TIGR00216 ispH_lytB (E)-4-hydroxy-3-methyl-but-2-enyl pyrophosphate reductase (IPP and DMAPP forming). Escherichia coli LytB protein had been found to regulate the activity of RelA (guanosine 3',5'-bispyrophosphate synthetase I), which in turn controls the level of a regulatory metabolite. It is involved in penicillin tolerance and the stringent response.
Probab=46.24 E-value=2.1e+02 Score=27.53 Aligned_cols=117 Identities=15% Similarity=0.151 Sum_probs=69.4
Q ss_pred CCCCCeEEEEe-ccccHhHHHHHHHHHHhCCC--eEEecCCCCCCCccccCCCCCCCCC------CCCCCeEEEecCCc-
Q 042576 34 YSDPGKLILAG-TIQFASAIRAAKPELEKQGF--KVMIPQSKPLSAGEVLGCTAPKIPA------RESDFNLVFIADGR- 103 (313)
Q Consensus 34 f~~~~~i~Lv~-tiQf~~~l~~~~~~L~~~g~--~v~ipq~~pls~GevLGCt~~~~~~------~~~~d~iv~igdGr- 103 (313)
++..+++++++ |.|-....+.+.+.|+.+++ ++.+. ..| |.+..... ...+|++++||+-.
T Consensus 150 l~~~~~v~vvsQTT~~~~~~~~i~~~l~~~~~~~~~~~~-------nTI--C~AT~~RQ~a~~~la~~vD~miVVGg~nS 220 (280)
T TIGR00216 150 FKVEDLLGVVSQTTLSQEDTKEIVAELKARVPQKEVPVF-------NTI--CYATQNRQDAVKELAPEVDLMIVIGGKNS 220 (280)
T ss_pred CCCCCcEEEEEcCCCcHHHHHHHHHHHHHhCCCcCCCCC-------CCc--ccccHHHHHHHHHHHhhCCEEEEECCCCC
Confidence 33346788776 66788888999999998773 32211 111 65543211 02489999998743
Q ss_pred ---ccHHHHHhhCCCceEEEeCCCCCcccccccChHHHHHHHHHHHHHHhhcCCEEEEEEeCCCCCCcHHHHHHHHHHHH
Q 042576 104 ---FHLEAFMISNPGIKTFRYDPYLGKLFLEEYDNKGMRETRKRAIEKAMKEARTWGIVLGTLGRQGNPRILERLQKRME 180 (313)
Q Consensus 104 ---FHle~~mi~np~~~~y~yDPys~~~~~e~~d~~~~l~~R~~~I~kak~~A~~~GIIvgTLg~Q~~~~ii~~l~~ll~ 180 (313)
-||..+.-.. ..++|..+-.. +.+. +..+ +.+++||.-|+ .---++++.+.+.|+
T Consensus 221 sNT~rL~ei~~~~-~~~t~~Ie~~~------el~~-----------~~l~-~~~~VGiTAGA---STP~~li~eVi~~l~ 278 (280)
T TIGR00216 221 SNTTRLYEIAEEH-GPPSYLIETAE------ELPE-----------EWLK-GVKVVGITAGA---STPDWIIEEVIRKIK 278 (280)
T ss_pred chHHHHHHHHHHh-CCCEEEECChH------HCCH-----------HHhC-CCCEEEEEecC---CCCHHHHHHHHHHHH
Confidence 2455555432 34666655331 2221 2335 77899998776 445567777777765
Q ss_pred H
Q 042576 181 K 181 (313)
Q Consensus 181 ~ 181 (313)
+
T Consensus 279 ~ 279 (280)
T TIGR00216 279 E 279 (280)
T ss_pred h
Confidence 3
No 109
>cd06297 PBP1_LacI_like_12 Ligand-binding domain of uncharacterized transcription regulators from Thermus thermophilus and close homologs. Ligand-binding domain of uncharacterized transcription regulators from Thermus thermophilus and close homologs from other bacteria. This group belongs to the the LacI-GalR family repressors that are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding.
Probab=45.69 E-value=39 Score=30.44 Aligned_cols=60 Identities=10% Similarity=0.173 Sum_probs=34.7
Q ss_pred EEEEEeCCCCCCcHHHHHHHHHHHHHcCCcEEEEEeCCCCH--HHHh-cC-cCCccEEEEecCC
Q 042576 156 WGIVLGTLGRQGNPRILERLQKRMEKKGFDYVVIMMSEISP--ARVA-LF-EDSVDAWIQIACP 215 (313)
Q Consensus 156 ~GIIvgTLg~Q~~~~ii~~l~~ll~~~Gkk~y~i~v~einp--~KLa-nf-~~~ID~fV~iaCP 215 (313)
+|+|+..+....+..+++.+++.+++.|....+.....-.. +-+. .+ ...+|++|+.++.
T Consensus 2 Igvi~p~~~~~~~~~~~~~i~~~~~~~gy~~~~~~~~~~~~~~~~~~~~l~~~~vdgvi~~~~~ 65 (269)
T cd06297 2 ISVLLPVVATEFYRRLLEGIEGALLEQRYDLALFPLLSLARLKRYLESTTLAYLTDGLLLASYD 65 (269)
T ss_pred EEEEeCCCcChhHHHHHHHHHHHHHHCCCEEEEEeCCCcHHHHHHHHHHHHhcCCCEEEEecCc
Confidence 67777666666667777777777777776666554432110 1111 12 1137777777653
No 110
>cd06290 PBP1_LacI_like_9 Ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. This group includes the ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.
Probab=45.54 E-value=2.1e+02 Score=25.22 Aligned_cols=131 Identities=14% Similarity=0.141 Sum_probs=60.6
Q ss_pred ccHhHHHHHHHHHHhCCCeEEecCCCCCCCc--cccCCCCCCCCCCCCCCeEEEecCCcccHHHHHhhCCCceEEEeCCC
Q 042576 47 QFASAIRAAKPELEKQGFKVMIPQSKPLSAG--EVLGCTAPKIPARESDFNLVFIADGRFHLEAFMISNPGIKTFRYDPY 124 (313)
Q Consensus 47 Qf~~~l~~~~~~L~~~g~~v~ipq~~pls~G--evLGCt~~~~~~~~~~d~iv~igdGrFHle~~mi~np~~~~y~yDPy 124 (313)
-|...++.+.+.+++.|+.+++.....-... +.+. .... ..+|++++.+...-...-..+.. .+|++.+|..
T Consensus 13 ~~~~~~~gi~~~~~~~gy~~~~~~~~~~~~~~~~~i~---~l~~--~~~dgiii~~~~~~~~~~~~~~~-~iPvV~i~~~ 86 (265)
T cd06290 13 FYGRILKGMERGLNGSGYSPIIATGHWNQSRELEALE---LLKS--RRVDALILLGGDLPEEEILALAE-EIPVLAVGRR 86 (265)
T ss_pred hHHHHHHHHHHHHHHCCCEEEEEeCCCCHHHHHHHHH---HHHH--CCCCEEEEeCCCCChHHHHHHhc-CCCEEEECCC
Confidence 3455566777888888888665221100000 0000 0001 13678777653211111112332 5788888753
Q ss_pred CC--cccccccChHHHHHHH-HHHHHHHhhcCCEEEEEEeCCCCCCcHHHHHHHHHHHHHcCCcE
Q 042576 125 LG--KLFLEEYDNKGMRETR-KRAIEKAMKEARTWGIVLGTLGRQGNPRILERLQKRMEKKGFDY 186 (313)
Q Consensus 125 s~--~~~~e~~d~~~~l~~R-~~~I~kak~~A~~~GIIvgTLg~Q~~~~ii~~l~~ll~~~Gkk~ 186 (313)
.. .+.....|..+.-+.= ..+++ + ..+.+++|.|........+-.+-.++.+++.|...
T Consensus 87 ~~~~~~~~V~~d~~~a~~~~~~~l~~--~-g~~~i~~i~~~~~~~~~~~r~~gf~~~~~~~~~~~ 148 (265)
T cd06290 87 VPGPGAASIAVDNFQGGYLATQHLID--L-GHRRIAHITGPRGHIDARDRLAGYRKALEEAGLEV 148 (265)
T ss_pred cCCCCCCEEEECcHHHHHHHHHHHHH--C-CCCeEEEEeCccccchhhHHHHHHHHHHHHcCCCC
Confidence 21 1211222322211110 11222 2 45789988877654443444555667777777653
No 111
>TIGR01007 eps_fam capsular exopolysaccharide family. This model describes the capsular exopolysaccharide proteins in bacteria. The exopolysaccharide gene cluster consists of several genes which encode a number of proteins which regulate the exoploysaccharide biosynthesis(EPS). Atleast 13 genes espA to espM in streptococcus species seem to direct the EPS proteins and all of which share high homology. Functional roles were characterized by gene disruption experiments which resulted in exopolysaccharide-deficient phenotypes.
Probab=45.42 E-value=68 Score=28.15 Aligned_cols=56 Identities=9% Similarity=0.132 Sum_probs=41.7
Q ss_pred HHHHHHHHHHHhhcCCEEEEEEeCCCCCCcHHHHHHHHHHHHHcCCcEEEEEeCCCCH
Q 042576 139 RETRKRAIEKAMKEARTWGIVLGTLGRQGNPRILERLQKRMEKKGFDYVVIMMSEISP 196 (313)
Q Consensus 139 l~~R~~~I~kak~~A~~~GIIvgTLg~Q~~~~ii~~l~~ll~~~Gkk~y~i~v~einp 196 (313)
.+.|..+..... +.+++ .|.|+.|+.|--.+.-.|-..+.++|+++.+|=++--+|
T Consensus 4 ~~l~~~l~~~~~-~~kvI-~v~s~kgG~GKTt~a~~LA~~la~~G~rVllID~D~~~~ 59 (204)
T TIGR01007 4 NAIRTNIQFSGA-EIKVL-LITSVKPGEGKSTTSANIAVAFAQAGYKTLLIDGDMRNS 59 (204)
T ss_pred HHHHHHHhhhcC-CCcEE-EEecCCCCCCHHHHHHHHHHHHHhCCCeEEEEeCCCCCh
Confidence 344555555555 66666 668999999999999999999999999977665554333
No 112
>cd06293 PBP1_LacI_like_11 Ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. This group includes the ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.
Probab=45.30 E-value=2.2e+02 Score=25.25 Aligned_cols=130 Identities=13% Similarity=0.094 Sum_probs=65.1
Q ss_pred ccHhHHHHHHHHHHhCCCeEEecCCCCCCCccccCCCCCCCCCCCCCCeEEEecCCcccHHHH-HhhCCCceEEEeCCCC
Q 042576 47 QFASAIRAAKPELEKQGFKVMIPQSKPLSAGEVLGCTAPKIPARESDFNLVFIADGRFHLEAF-MISNPGIKTFRYDPYL 125 (313)
Q Consensus 47 Qf~~~l~~~~~~L~~~g~~v~ipq~~pls~GevLGCt~~~~~~~~~~d~iv~igdGrFHle~~-mi~np~~~~y~yDPys 125 (313)
.|...++.+.+.+++.|+++.+-....-...|.- . ...+.. ..+|++++.+.-. ....+ .+.....|++.+|...
T Consensus 13 ~~~~~~~gi~~~~~~~gy~v~~~~~~~~~~~~~~-~-i~~~~~-~~~dgiii~~~~~-~~~~~~~~~~~~~pvV~i~~~~ 88 (269)
T cd06293 13 FFAELADAVEEEADARGLSLVLCATRNRPERELT-Y-LRWLDT-NHVDGLIFVTNRP-DDGALAKLINSYGNIVLVDEDV 88 (269)
T ss_pred cHHHHHHHHHHHHHHCCCEEEEEeCCCCHHHHHH-H-HHHHHH-CCCCEEEEeCCCC-CHHHHHHHHhcCCCEEEECCCC
Confidence 4566778888899999998765211100000000 0 000000 2378888875321 11211 2223467888888532
Q ss_pred C--cccccccChH---HHHHHHHHHHHHHhhcCCEEEEEEeCCCCCCcHHHHHHHHHHHHHcCCc
Q 042576 126 G--KLFLEEYDNK---GMRETRKRAIEKAMKEARTWGIVLGTLGRQGNPRILERLQKRMEKKGFD 185 (313)
Q Consensus 126 ~--~~~~e~~d~~---~~l~~R~~~I~kak~~A~~~GIIvgTLg~Q~~~~ii~~l~~ll~~~Gkk 185 (313)
. .+.....|.. +....+ +++ + .-+++|+|.|.........-.+-.++-++++|..
T Consensus 89 ~~~~~~~V~~d~~~~~~~~~~~--L~~--~-G~~~i~~i~~~~~~~~~~~R~~Gf~~a~~~~~~~ 148 (269)
T cd06293 89 PGAKVPKVFCDNEQGGRLATRH--LAR--A-GHRRIAFVGGPDALISARERYAGYREALAEAHIP 148 (269)
T ss_pred CCCCCCEEEECCHHHHHHHHHH--HHH--C-CCceEEEEecCcccccHHHHHHHHHHHHHHcCCC
Confidence 1 1111222322 222222 222 3 5678999988765544444456677778888764
No 113
>PF02401 LYTB: LytB protein; InterPro: IPR003451 Terpenes are among the largest groups of natural products and include compounds such as vitamins, cholesterol and carotenoids. The biosynthesis of all terpenoids begins with one or both of the two C5 precursors of the pathway: isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP). In animals, fungi, and certain bacteria, the synthesis of IPP and DMAPP occurs via the well-known mevalonate pathway, however, a second, nonmevalonate terpenoid pathway has been identified in many eubacteria, algae and the chloroplasts of higher plants []. LytB(IspH) catalyses the conversion of 1-hydroy-2-methyl-2-(E)-butenyl 4-diphosphate into IPP and DMAPP in this second pathway The enzyme appears to be responsible for a branch-step in the nonmevalonate pathway, in that IPP and DMAPP are produced in parallel from a single precursor although the exact mechanism of this is not currently fully understood []. Escherichia coli LytB protein had been found to regulate the activity of RelA (guanosine 3',5'-bispyrophosphate synthetase I), which in turn controls the level of a regulatory metabolite. It is involved in penicillin tolerance and the stringent response [].; GO: 0019288 isopentenyl diphosphate biosynthetic process, mevalonate-independent pathway, 0055114 oxidation-reduction process; PDB: 3DNF_B 3SZL_B 3KE8_B 3KEF_B 3SZU_A 3KEL_A 3F7T_B 3KE9_B 3KEM_B 3T0G_A ....
Probab=45.11 E-value=1.4e+02 Score=28.76 Aligned_cols=119 Identities=19% Similarity=0.212 Sum_probs=0.0
Q ss_pred CCCCCeEEEEe-ccccHhHHHHHHHHHHhCCCeEEecCCCCCCCccccCCCCCCCCCC------CCCCeEEEecCCccc-
Q 042576 34 YSDPGKLILAG-TIQFASAIRAAKPELEKQGFKVMIPQSKPLSAGEVLGCTAPKIPAR------ESDFNLVFIADGRFH- 105 (313)
Q Consensus 34 f~~~~~i~Lv~-tiQf~~~l~~~~~~L~~~g~~v~ipq~~pls~GevLGCt~~~~~~~------~~~d~iv~igdGrFH- 105 (313)
+...+++++++ |.+=....+.+.+.|+++++++..+-.+.. |.+...... ..+|++++||+-...
T Consensus 151 ~~~~~kv~vvsQTT~~~~~~~~i~~~l~~~~~~~~~~~~nTI-------C~aT~~RQ~a~~~La~~vD~miVIGg~~SsN 223 (281)
T PF02401_consen 151 ISDPKKVAVVSQTTQSVEKFEEIVEALKKRFPELEGPVFNTI-------CYATQNRQEAARELAKEVDAMIVIGGKNSSN 223 (281)
T ss_dssp GSSTTCEEEEE-TTS-HHHHHHHHHHHHHHSTCEE-SCC-S---------CHHHHHHHHHHHHHCCSSEEEEES-TT-HH
T ss_pred CCCCCeEEEEEeecccHHHHHHHHHHHHHhCccccCCCCCCC-------CHhHHHHHHHHHHHHhhCCEEEEecCCCCcc
Q ss_pred ---HHHHHhhCCCceEEEeCCCCCcccccccChHHHHHHHHHHHHHHhhcCCEEEEEEeCCCCCCcHHHHHHHHHHHHH
Q 042576 106 ---LEAFMISNPGIKTFRYDPYLGKLFLEEYDNKGMRETRKRAIEKAMKEARTWGIVLGTLGRQGNPRILERLQKRMEK 181 (313)
Q Consensus 106 ---le~~mi~np~~~~y~yDPys~~~~~e~~d~~~~l~~R~~~I~kak~~A~~~GIIvgTLg~Q~~~~ii~~l~~ll~~ 181 (313)
|..+.-.. ..++|..+-.. ----+..+ ..+++||.-|+ .---++++.+.+.|++
T Consensus 224 T~kL~eia~~~-~~~t~~Ie~~~-----------------el~~~~l~-~~~~VGItaGA---STP~~ii~eVi~~l~~ 280 (281)
T PF02401_consen 224 TRKLAEIAKEH-GKPTYHIETAD-----------------ELDPEWLK-GVKKVGITAGA---STPDWIIEEVIDRLEE 280 (281)
T ss_dssp HHHHHHHHHHC-TTCEEEESSGG-----------------G--HHHHT-T-SEEEEEE-T---TS-HHHHHHHHHHHHH
T ss_pred HHHHHHHHHHh-CCCEEEeCCcc-----------------ccCHhHhC-CCCEEEEEccC---CCCHHHHHHHHHHHhc
No 114
>cd06294 PBP1_ycjW_transcription_regulator_like Ligand-binding domain of uncharacterized transcription regulator ycjW which is a member of the LacI-GalR family repressors. This group includes the ligand-binding domain of uncharacterized transcription regulator ycjW which is a member of the LacI-GalR family repressors that are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.
Probab=44.88 E-value=45 Score=29.59 Aligned_cols=32 Identities=19% Similarity=0.297 Sum_probs=18.1
Q ss_pred EEEEEeC-----CCCCCcHHHHHHHHHHHHHcCCcEE
Q 042576 156 WGIVLGT-----LGRQGNPRILERLQKRMEKKGFDYV 187 (313)
Q Consensus 156 ~GIIvgT-----Lg~Q~~~~ii~~l~~ll~~~Gkk~y 187 (313)
+|+|+.. +.-..+..+++.+++.+++.|.+..
T Consensus 2 igli~p~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~ 38 (270)
T cd06294 2 IGVVLPPSADEAFQNPFFIEVLRGISAVANENGYDIS 38 (270)
T ss_pred EEEEeCCccccCcCCCCHHHHHHHHHHHHHHCCCEEE
Confidence 5666654 3334455566666666666665543
No 115
>PLN02404 6,7-dimethyl-8-ribityllumazine synthase
Probab=44.69 E-value=76 Score=27.46 Aligned_cols=87 Identities=22% Similarity=0.209 Sum_probs=53.8
Q ss_pred CCEEEEEEeCCCCCCcHHHHHHHHHHHHHcCCc---EEEEEeC---CCC--HHHHhcCcCCccEEEEecCCC-ccc----
Q 042576 153 ARTWGIVLGTLGRQGNPRILERLQKRMEKKGFD---YVVIMMS---EIS--PARVALFEDSVDAWIQIACPR-LSI---- 219 (313)
Q Consensus 153 A~~~GIIvgTLg~Q~~~~ii~~l~~ll~~~Gkk---~y~i~v~---ein--p~KLanf~~~ID~fV~iaCPr-lsi---- 219 (313)
.-+||||++..-..-.-.+++-..+.|+++|.+ ..++.|- ||- ..+|+.-. ++|++|-++|=- ...
T Consensus 7 ~~ri~IV~s~fn~~I~~~Ll~ga~~~l~~~gv~~~~i~v~~VPGa~EiP~a~~~l~~s~-~~DavIaLG~VIrGeT~H~e 85 (141)
T PLN02404 7 GLRFGVVVARFNEIITKNLLEGALETFKRYSVKEENIDVVWVPGSFEIPVVAQRLAKSG-KYDAILCIGAVIRGDTTHYD 85 (141)
T ss_pred CCEEEEEEecCcHHHHHHHHHHHHHHHHHcCCCccceEEEEcCcHHHHHHHHHHHHhcC-CCCEEEEEEEEEeCCCchhH
Confidence 458999998654444444455555678888864 4555553 222 25676666 699999999931 111
Q ss_pred -----------cccCCCCCc----ccCHHHHHHHhC
Q 042576 220 -----------DWGDAFTKP----LLTPFEAEIALG 240 (313)
Q Consensus 220 -----------d~~~~f~kP----vLTPyE~~vAL~ 240 (313)
+=+-++.+| ||||--.+-|+.
T Consensus 86 ~V~~~v~~gl~~vsl~~~~PV~~GVLt~~~~eQA~~ 121 (141)
T PLN02404 86 AVANSAASGVLSAGLNSGVPCIFGVLTCDDMEQALN 121 (141)
T ss_pred HHHHHHHHHHHHHHhccCCCEEEEEcCCCCHHHHHH
Confidence 123357788 477776666663
No 116
>cd01536 PBP1_ABC_sugar_binding_like Periplasmic sugar-binding domain of active transport systems that are members of the type I periplasmic binding protein (PBP1) superfamily. Periplasmic sugar-binding domain of active transport systems that are members of the type I periplasmic binding protein (PBP1) superfamily. The members of this family function as the primary receptors for chemotaxis and transport of many sugar based solutes in bacteria and archaea. The sugar binding domain is also homologous to the ligand-binding domain of eukaryotic receptors such as glutamate receptor (GluR) and DNA-binding transcriptional repressors such as LacI and GalR. Moreover, this periplasmic binding domain, also known as Venus flytrap domain, undergoes transition from an open to a closed conformational state upon the binding of ligands such as lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars. This family also includes the periplasmic binding domain of autoinducer-2 (AI-2
Probab=44.53 E-value=2.1e+02 Score=24.86 Aligned_cols=146 Identities=10% Similarity=0.105 Sum_probs=68.3
Q ss_pred ccHhHHHHHHHHHHhCCCeEEecCCCCCCCccccCCCCCCCCCCCCCCeEEEecCCc-ccHHHH-HhhCCCceEEEeCCC
Q 042576 47 QFASAIRAAKPELEKQGFKVMIPQSKPLSAGEVLGCTAPKIPARESDFNLVFIADGR-FHLEAF-MISNPGIKTFRYDPY 124 (313)
Q Consensus 47 Qf~~~l~~~~~~L~~~g~~v~ipq~~pls~GevLGCt~~~~~~~~~~d~iv~igdGr-FHle~~-mi~np~~~~y~yDPy 124 (313)
.|...++.+.+.++++|+++.+-.... .+..-..+-..... ..+|+++..+... .+...+ .+....+|+...+..
T Consensus 13 ~~~~~~~~~~~~a~~~g~~~~~~~~~~-~~~~~~~~~~~l~~--~~vdgvi~~~~~~~~~~~~~~~l~~~~ip~V~~~~~ 89 (267)
T cd01536 13 FWQAMNKGAEAAAKELGVELIVLDAQN-DVSKQIQQIEDLIA--QGVDGIIISPVDSAALTPALKKANAAGIPVVTVDSD 89 (267)
T ss_pred HHHHHHHHHHHHHHhcCceEEEECCCC-CHHHHHHHHHHHHH--cCCCEEEEeCCCchhHHHHHHHHHHCCCcEEEecCC
Confidence 445566677777887888865421110 01000000000011 1368877665322 111111 122346677666542
Q ss_pred C---CcccccccChHHHHHH-HHHHHHHHhhcCCEEEEEEeCCCCCCcHHHHHHHHHHHHHcC-CcEEEEEeCCCCH
Q 042576 125 L---GKLFLEEYDNKGMRET-RKRAIEKAMKEARTWGIVLGTLGRQGNPRILERLQKRMEKKG-FDYVVIMMSEISP 196 (313)
Q Consensus 125 s---~~~~~e~~d~~~~l~~-R~~~I~kak~~A~~~GIIvgTLg~Q~~~~ii~~l~~ll~~~G-kk~y~i~v~einp 196 (313)
. ..+.....|....-+. =..++++.. ..+++|+|.+...........+-.++-++++| .....+.....++
T Consensus 90 ~~~~~~~~~v~~d~~~~~~~~~~~l~~~~~-g~~~i~~i~~~~~~~~~~~r~~gf~~~~~~~~~~~~~~~~~~~~~~ 165 (267)
T cd01536 90 IDGGNRLAYVGTDNYEAGRLAGEYLAKLLG-GKGKVAIIEGPPGSSNAQERVKGFRDALKEYPDIEIVAVQDGNWDR 165 (267)
T ss_pred CCccceeEEEecCHHHHHHHHHHHHHHHhC-CCceEEEEEcccccchHHHHHHHHHHHHHhCCCcEEEEEecCCCcH
Confidence 2 1222222333222111 123334444 56889999876543344456677788888884 5544444444443
No 117
>TIGR00640 acid_CoA_mut_C methylmalonyl-CoA mutase C-terminal domain. Methylmalonyl-CoA mutase (EC 5.4.99.2) catalyzes a reversible isomerization between L-methylmalonyl-CoA and succinyl-CoA. The enzyme uses an adenosylcobalamin cofactor. It may be a homodimer, as in mitochondrion, or a heterodimer with partially homologous beta chain that does not bind the adenosylcobalamin cofactor, as in Propionibacterium freudenreichii. The most similar archaeal sequences are separate chains, such as AF2215 and AF2219 of Archaeoglobus fulgidus, that correspond roughly to the first 500 and last 130 residues, respectively of known methylmalonyl-CoA mutases. This model describes the C-terminal domain subfamily. In a neighbor-joining tree (methylaspartate mutase S chain as the outgroup), AF2219 branches with a coenzyme B12-dependent enzyme known not to be 5.4.99.2.
Probab=44.34 E-value=60 Score=27.39 Aligned_cols=71 Identities=18% Similarity=0.278 Sum_probs=44.9
Q ss_pred HHHHHhhcCCEEEEEEeCCCCCCcHHHHHHHHHHHHHcCCcEEEEEeCC-CCHHHHhcCc-CCccEEEEecCCCc
Q 042576 145 AIEKAMKEARTWGIVLGTLGRQGNPRILERLQKRMEKKGFDYVVIMMSE-ISPARVALFE-DSVDAWIQIACPRL 217 (313)
Q Consensus 145 ~I~kak~~A~~~GIIvgTLg~Q~~~~ii~~l~~ll~~~Gkk~y~i~v~e-inp~KLanf~-~~ID~fV~iaCPrl 217 (313)
.++.|+ +.+-=.|.++++- ..+.+.+..+.+.|+++|.....+++|- +-++..+.|. -.+|.|+-.++|-.
T Consensus 45 ~v~aa~-e~~adii~iSsl~-~~~~~~~~~~~~~L~~~g~~~i~vivGG~~~~~~~~~l~~~Gvd~~~~~gt~~~ 117 (132)
T TIGR00640 45 IARQAV-EADVHVVGVSSLA-GGHLTLVPALRKELDKLGRPDILVVVGGVIPPQDFDELKEMGVAEIFGPGTPIP 117 (132)
T ss_pred HHHHHH-HcCCCEEEEcCch-hhhHHHHHHHHHHHHhcCCCCCEEEEeCCCChHhHHHHHHCCCCEEECCCCCHH
Confidence 455665 3333334446664 5688889999999999988666677773 3333344442 14888877666543
No 118
>COG1111 MPH1 ERCC4-like helicases [DNA replication, recombination, and repair]
Probab=44.14 E-value=89 Score=32.70 Aligned_cols=47 Identities=19% Similarity=0.325 Sum_probs=37.7
Q ss_pred hHHHHHHHHHhCC--CCCeEEEEeccccHhHHHHHHHHHHhCCCeE---EecCC
Q 042576 23 VNRLIDTIKVNYS--DPGKLILAGTIQFASAIRAAKPELEKQGFKV---MIPQS 71 (313)
Q Consensus 23 ~~~~i~~i~~~f~--~~~~i~Lv~tiQf~~~l~~~~~~L~~~g~~v---~ipq~ 71 (313)
++++.+.++++|. +++++.+++ ||..+.+.+.+.|.+.|.++ +|+|.
T Consensus 350 l~~l~eilke~~~k~~~~RvIVFT--~yRdTae~i~~~L~~~~~~~~~rFiGQa 401 (542)
T COG1111 350 LEKLREILKEQLEKNGDSRVIVFT--EYRDTAEEIVNFLKKIGIKARVRFIGQA 401 (542)
T ss_pred HHHHHHHHHHHHhcCCCceEEEEe--hhHhHHHHHHHHHHhcCCcceeEEeecc
Confidence 5678888888884 456777776 89999999999999988774 56775
No 119
>PF02514 CobN-Mg_chel: CobN/Magnesium Chelatase; InterPro: IPR003672 This family contains a domain common to the cobN protein and to magnesium protoporphyrin chelatase. CobN may play a role in cobalt insertion reactions and is implicated in the conversion of precorrin-2 to cobyrinic acid in cobalamin biosynthesis []. Magnesium protoporphyrin chelatase is involved in chlorophyll biosynthesis as the third subunit of light-independent protochlorophyllide reductase in bacteria and plants [].; GO: 0009058 biosynthetic process
Probab=44.07 E-value=34 Score=38.87 Aligned_cols=94 Identities=21% Similarity=0.299 Sum_probs=65.6
Q ss_pred cCCEEEEEEeCCC-CCCcHHHHHHHHHHHHHcCCcEEEEEeCC--CCHHHHh-cCc----CCccEEEEecCCCccc----
Q 042576 152 EARTWGIVLGTLG-RQGNPRILERLQKRMEKKGFDYVVIMMSE--ISPARVA-LFE----DSVDAWIQIACPRLSI---- 219 (313)
Q Consensus 152 ~A~~~GIIvgTLg-~Q~~~~ii~~l~~ll~~~Gkk~y~i~v~e--inp~KLa-nf~----~~ID~fV~iaCPrlsi---- 219 (313)
++.+||||+..-- ..|+...++.|-+.|+++|..++.++.+- -..+.+. -|. ..||+.|.+.+=++.-
T Consensus 70 ~~P~VgIlfyrs~~~~g~~~~vdaLI~~LE~~G~nvipvf~~~~~~~~~~i~~~f~~~g~~~vDaIIn~~~f~l~~~~~~ 149 (1098)
T PF02514_consen 70 NRPTVGILFYRSYWLSGNTAVVDALIRALEERGLNVIPVFCSSGPDSQEAIEDYFMDDGKPRVDAIINLTGFSLGGGPAG 149 (1098)
T ss_pred CCCEEEEEeehhhhhcCCcHHHHHHHHHHHHCCCeEEEEEecCccchHHHHHHHHhhcCCCCceEEEEcCccccCCCCcc
Confidence 6889999996543 34688999999999999999999999753 3333343 333 1399999988877543
Q ss_pred ---cccCCCCCcccCHHHHHHHhCCCCccccc
Q 042576 220 ---DWGDAFTKPLLTPFEAEIALGVIPGWWER 248 (313)
Q Consensus 220 ---d~~~~f~kPvLTPyE~~vAL~~~~~~w~~ 248 (313)
.+.+...-|||.+.-. .......|+.
T Consensus 150 ~~~~~L~~LnVPVlq~i~~---~~~t~eeW~~ 178 (1098)
T PF02514_consen 150 GAIELLKELNVPVLQAITL---YYQTREEWEE 178 (1098)
T ss_pred hhHHHHHHCCCCEEEeecc---CCCCHHHHHh
Confidence 3456778898887643 1223345654
No 120
>PRK09271 flavodoxin; Provisional
Probab=43.56 E-value=80 Score=27.02 Aligned_cols=58 Identities=12% Similarity=0.098 Sum_probs=36.8
Q ss_pred EEEEEEeCCCCCCcHHHHHHHHHHHHHcCCcEEEEEeCCCCHHH-HhcCcCCccEEEEecCC
Q 042576 155 TWGIVLGTLGRQGNPRILERLQKRMEKKGFDYVVIMMSEISPAR-VALFEDSVDAWIQIACP 215 (313)
Q Consensus 155 ~~GIIvgTLg~Q~~~~ii~~l~~ll~~~Gkk~y~i~v~einp~K-Lanf~~~ID~fV~iaCP 215 (313)
++.|+.+|..| +...++++|.+.|++.|.++-+.-++...... ...+. +.|++ +++||
T Consensus 2 kv~IvY~S~tG-nTe~~A~~ia~~l~~~g~~v~~~~~~~~~~~~~~~~~~-~~d~v-ilgt~ 60 (160)
T PRK09271 2 RILLAYASLSG-NTREVAREIEERCEEAGHEVDWVETDVQTLAEYPLDPE-DYDLY-LLGTW 60 (160)
T ss_pred eEEEEEEcCCc-hHHHHHHHHHHHHHhCCCeeEEEecccccccccccCcc-cCCEE-EEECc
Confidence 47899999653 45679999999999999877555544433222 12333 35664 45555
No 121
>cd06316 PBP1_ABC_sugar_binding_like_7 Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems. Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily, which consists of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis.
Probab=43.47 E-value=2.6e+02 Score=25.45 Aligned_cols=41 Identities=5% Similarity=-0.067 Sum_probs=25.3
Q ss_pred HHHHHHHhhcCCEEEEEEeCCCCCCcHHHHHHHHHHHHHcCC
Q 042576 143 KRAIEKAMKEARTWGIVLGTLGRQGNPRILERLQKRMEKKGF 184 (313)
Q Consensus 143 ~~~I~kak~~A~~~GIIvgTLg~Q~~~~ii~~l~~ll~~~Gk 184 (313)
..++++.+ ..+++++|.|..+......-.+-.++-|++++-
T Consensus 117 ~~l~~~~~-g~~~i~~l~~~~~~~~~~~R~~gf~~~l~~~~~ 157 (294)
T cd06316 117 DALAKALP-GKGKVGLIYHGADYFVTNQRDQGFKETIKKNYP 157 (294)
T ss_pred HHHHHHhC-CCceEEEEeCCCCcccHHHHHHHHHHHHHHhCC
Confidence 44555656 678999998766544333445556666666653
No 122
>cd06305 PBP1_methylthioribose_binding_like Methylthioribose-binding protein-like of ABC-type transport systems that belong to a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein (PBP1) superfamily. Methylthioribose-binding protein-like of ABC-type transport systems that belong to a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein (PBP1) superfamily, which consists of two alpha/beta globular domains connected by a three-stranded hinge. This Venus flytrap-like domain undergoes transition from an open to a closed conformational state upon ligand binding. The sugar-binding domain of the periplasmic proteins in this group is also homologous to the ligand-binding domain of eukaryotic receptors such as metabotropic glutamate receptor (mGluR), DNA-binding transcriptional repressors such as LacI and GalR.
Probab=43.29 E-value=68 Score=28.57 Aligned_cols=33 Identities=18% Similarity=0.007 Sum_probs=19.3
Q ss_pred EEEEEeCCCCCCcHHHHHHHHHHHHHcCCcEEE
Q 042576 156 WGIVLGTLGRQGNPRILERLQKRMEKKGFDYVV 188 (313)
Q Consensus 156 ~GIIvgTLg~Q~~~~ii~~l~~ll~~~Gkk~y~ 188 (313)
+|+|+.++.-.....+++.+++.+++.|....+
T Consensus 2 Ig~i~~~~~~~~~~~~~~gi~~~~~~~g~~~~~ 34 (273)
T cd06305 2 IAVVRYGGSGDFDQAYLAGTKAEAEALGGDLRV 34 (273)
T ss_pred eEEEeecCCCcHHHHHHHHHHHHHHHcCCEEEE
Confidence 566666555444555666666666666655443
No 123
>PRK10423 transcriptional repressor RbsR; Provisional
Probab=43.14 E-value=2.3e+02 Score=26.09 Aligned_cols=138 Identities=13% Similarity=0.156 Sum_probs=69.1
Q ss_pred eEEEEec----cccHhHHHHHHHHHHhCCCeEEecCCC--CCCCccccCCCCCCCCCCCCCCeEEEecCCcc-cHHHHHh
Q 042576 39 KLILAGT----IQFASAIRAAKPELEKQGFKVMIPQSK--PLSAGEVLGCTAPKIPARESDFNLVFIADGRF-HLEAFMI 111 (313)
Q Consensus 39 ~i~Lv~t----iQf~~~l~~~~~~L~~~g~~v~ipq~~--pls~GevLGCt~~~~~~~~~~d~iv~igdGrF-Hle~~mi 111 (313)
.|+++.. --|...++.+.+.+.+.|+++++-... +-...+.+. .+.. ..+|++|+.+.... -...++-
T Consensus 58 ~Igvi~~~~~~~~~~~~~~gi~~~~~~~g~~~~~~~~~~~~~~~~~~~~----~l~~-~~vdGiI~~~~~~~~~~~~~l~ 132 (327)
T PRK10423 58 TIGMLITASTNPFYSELVRGVERSCFERGYSLVLCNTEGDEQRMNRNLE----TLMQ-KRVDGLLLLCTETHQPSREIMQ 132 (327)
T ss_pred eEEEEeCCCCCCcHHHHHHHHHHHHHHcCCEEEEEeCCCCHHHHHHHHH----HHHH-cCCCEEEEeCCCcchhhHHHHH
Confidence 4776642 246666778889999999997652211 100001110 0001 23788887754311 1111222
Q ss_pred hCCCceEEEeCCC--CCcccccccCh---HHHHHHHHHHHHHHhhcCCEEEEEEeCCCCCCcHHHHHHHHHHHHHcCCcE
Q 042576 112 SNPGIKTFRYDPY--LGKLFLEEYDN---KGMRETRKRAIEKAMKEARTWGIVLGTLGRQGNPRILERLQKRMEKKGFDY 186 (313)
Q Consensus 112 ~np~~~~y~yDPy--s~~~~~e~~d~---~~~l~~R~~~I~kak~~A~~~GIIvgTLg~Q~~~~ii~~l~~ll~~~Gkk~ 186 (313)
.....|+..+|-. .........|. .++... ++++ + .-+++|+|.|.........-.+-.++-++++|.+.
T Consensus 133 ~~~~iPvV~i~~~~~~~~~~~v~~d~~~~~~~a~~--~L~~--~-G~~~I~~i~~~~~~~~~~~R~~Gf~~al~~~~~~~ 207 (327)
T PRK10423 133 RYPSVPTVMMDWAPFDGDSDLIQDNSLLGGDLATQ--YLID--K-GYTRIACITGPLDKTPARLRLEGYRAAMKRAGLNI 207 (327)
T ss_pred hcCCCCEEEECCccCCCCCCEEEEChHHHHHHHHH--HHHH--c-CCCeEEEEeCCccccchHHHHHHHHHHHHHcCCCC
Confidence 2246788877732 11111111221 111111 2222 3 56899999876554333445566777888888653
No 124
>PRK05443 polyphosphate kinase; Provisional
Probab=42.97 E-value=4.7e+02 Score=28.40 Aligned_cols=92 Identities=17% Similarity=0.317 Sum_probs=58.3
Q ss_pred eEEEecCCcccHHHHHhhCCCceEEEeCCCC---------------C-----cccccccC-hHHHHHHHHHHHHHHhhcC
Q 042576 95 NLVFIADGRFHLEAFMISNPGIKTFRYDPYL---------------G-----KLFLEEYD-NKGMRETRKRAIEKAMKEA 153 (313)
Q Consensus 95 ~iv~igdGrFHle~~mi~np~~~~y~yDPys---------------~-----~~~~e~~d-~~~~l~~R~~~I~kak~~A 153 (313)
.+.+||.|.||..++.+. .+..++.+||-- . .+.....+ ..++++.=...|+.|+ ..
T Consensus 451 ~~~~iGTgN~n~~s~~~y-~D~~l~t~d~~i~~d~~~~F~~l~~~~~~~~~~~l~~sP~~~~~~l~~~i~~ei~~Ak-~G 528 (691)
T PRK05443 451 RYVHLGTGNYNPKTARLY-TDLSLLTADPEIGEDVTRLFNYLTGYSRPVKLRKLLVSPFTLRERLLELIDREIANAR-AG 528 (691)
T ss_pred EEEEEcCCCCCcchhhhc-cceeEEEeChHHHHHHHHHHHHHhCcCccccccEEeecCccHHHHHHHHHHHHHHHHh-cC
Confidence 367899999998888774 688888888721 1 11111111 2333433345677777 65
Q ss_pred CEEEEEEeCCCCCCcHHHHHHHHHHHHHcCCcEEEEE
Q 042576 154 RTWGIVLGTLGRQGNPRILERLQKRMEKKGFDYVVIM 190 (313)
Q Consensus 154 ~~~GIIvgTLg~Q~~~~ii~~l~~ll~~~Gkk~y~i~ 190 (313)
+.=.|++-|-... ...+++.|.... ++|.++-+++
T Consensus 529 ~~a~I~ik~n~l~-d~~ii~aL~~As-~~GV~V~liV 563 (691)
T PRK05443 529 KPARIIAKMNSLV-DPQIIDALYEAS-QAGVKIDLIV 563 (691)
T ss_pred CCCEEEEEcCCCC-CHHHHHHHHHHH-HCCCeEEEEE
Confidence 5445566555544 788888887654 5799988887
No 125
>PRK14571 D-alanyl-alanine synthetase A; Provisional
Probab=42.95 E-value=88 Score=29.34 Aligned_cols=60 Identities=23% Similarity=0.317 Sum_probs=45.5
Q ss_pred EEEEEEeCCCCCC--cHHHHHHHHHHHHHcCCcEEEEEeCCCCHHHHhcCcCCccEEEEecCCC
Q 042576 155 TWGIVLGTLGRQG--NPRILERLQKRMEKKGFDYVVIMMSEISPARVALFEDSVDAWIQIACPR 216 (313)
Q Consensus 155 ~~GIIvgTLg~Q~--~~~ii~~l~~ll~~~Gkk~y~i~v~einp~KLanf~~~ID~fV~iaCPr 216 (313)
+++||+|-.+... ++.-.+.+.+-|++.|.++..+-..+-...++.... ++|+ |...|+.
T Consensus 2 ~v~v~~gg~s~e~~~sl~s~~~i~~al~~~g~~~~~i~~~~~~~~~~~~~~-~~D~-v~~~~~g 63 (299)
T PRK14571 2 RVALLMGGVSREREISLRSGERVKKALEKLGYEVTVFDVDEDFLKKVDQLK-SFDV-VFNVLHG 63 (299)
T ss_pred eEEEEeCCCCCCccchHHHHHHHHHHHHHcCCeEEEEccCchHHHHhhhcc-CCCE-EEEeCCC
Confidence 5899999877554 566788999999999999988887766666776666 6885 4555554
No 126
>cd06285 PBP1_LacI_like_7 Ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. This group includes the ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.
Probab=42.83 E-value=1e+02 Score=27.35 Aligned_cols=60 Identities=17% Similarity=0.269 Sum_probs=38.0
Q ss_pred EEEEEEeCCCCCCcHHHHHHHHHHHHHcCCcEEEEEeCCCCHHHHh----cC-cCCccEEEEecCC
Q 042576 155 TWGIVLGTLGRQGNPRILERLQKRMEKKGFDYVVIMMSEISPARVA----LF-EDSVDAWIQIACP 215 (313)
Q Consensus 155 ~~GIIvgTLg~Q~~~~ii~~l~~ll~~~Gkk~y~i~v~einp~KLa----nf-~~~ID~fV~iaCP 215 (313)
+||+|+..+.......+++.+.+.+++.|.+..+ ..+.-++++.. .+ ...+|+.++..|-
T Consensus 1 ~igvi~p~~~~~~~~~~~~gi~~~~~~~~~~~~~-~~~~~~~~~~~~~i~~l~~~~~dgiii~~~~ 65 (265)
T cd06285 1 TIGVLVPRLTDTVMATMYEGIEEAAAERGYSTFV-ANTGDNPDAQRRAIEMLLDRRVDGLILGDAR 65 (265)
T ss_pred CEEEEeCCCCCccHHHHHHHHHHHHHHCCCEEEE-EeCCCCHHHHHHHHHHHHHcCCCEEEEecCC
Confidence 4788888777777777888888888888877543 34444544321 11 1137888776553
No 127
>PRK10355 xylF D-xylose transporter subunit XylF; Provisional
Probab=42.80 E-value=78 Score=30.17 Aligned_cols=63 Identities=14% Similarity=0.101 Sum_probs=45.4
Q ss_pred cCCEEEEEEeCCCCCCcHHHHHHHHHHHHHcCCcEEEEEeCCCCHHHHh----cCc-CCccEEEEecCC
Q 042576 152 EARTWGIVLGTLGRQGNPRILERLQKRMEKKGFDYVVIMMSEISPARVA----LFE-DSVDAWIQIACP 215 (313)
Q Consensus 152 ~A~~~GIIvgTLg~Q~~~~ii~~l~~ll~~~Gkk~y~i~v~einp~KLa----nf~-~~ID~fV~iaCP 215 (313)
++.++|+++..+.-.....+++-+++.++++|....+.. +.-++++.. ++. ..+|++|++++.
T Consensus 24 ~~~~Ig~i~~~~~~~f~~~~~~gi~~~a~~~g~~l~i~~-~~~~~~~~~~~i~~l~~~~vDGiIi~~~~ 91 (330)
T PRK10355 24 KEVKIGMAIDDLRLERWQKDRDIFVKKAESLGAKVFVQS-ANGNEETQMSQIENMINRGVDVLVIIPYN 91 (330)
T ss_pred CCceEEEEecCCCchHHHHHHHHHHHHHHHcCCEEEEEC-CCCCHHHHHHHHHHHHHcCCCEEEEeCCC
Confidence 357899999988888888999999999999997765543 334554332 221 148999988764
No 128
>cd05569 PTS_IIB_fructose PTS_IIB_fructose: subunit IIB of enzyme II (EII) of the fructose-specific phosphoenolpyruvate:carbohydrate phosphotransferase system (PTS). In this system, EII (also referred to as FruAB) is a fructose-specific permease made up of two proteins (FruA and FruB) each containing 3 domains. The FruA protein contains two tandem nonidentical IIB domains and a C-terminal IIC transmembrane domain. Both IIB domains of FruA are included in this alignment. The FruB protein (also referred to as diphosphoryl transfer protein) contains a IIA domain, a domain of unknown function, and an Hpr-like domain called FPr (fructose-inducible HPr). This familiy also includes the IIB domains of several fructose-like PTS permeases including the Frv permease encoded by the frvABXR operon, the Frw permease encoded by the frwACBD operon, the Frx permease encoded by the hrsA gene, and the Fry permease encoded by the fryABC (ypdDGH) operon. FruAB takes up exogenous fructose, releasing the 1-p
Probab=42.68 E-value=1e+02 Score=24.44 Aligned_cols=68 Identities=24% Similarity=0.222 Sum_probs=49.2
Q ss_pred EEEEEeCCCCCCcHHHHHHHHHHHHHcCCcEEEEE------eCCCCHHHHhcCcCCccEEEEecCCCccccccCCC-CCc
Q 042576 156 WGIVLGTLGRQGNPRILERLQKRMEKKGFDYVVIM------MSEISPARVALFEDSVDAWIQIACPRLSIDWGDAF-TKP 228 (313)
Q Consensus 156 ~GIIvgTLg~Q~~~~ii~~l~~ll~~~Gkk~y~i~------v~einp~KLanf~~~ID~fV~iaCPrlsid~~~~f-~kP 228 (313)
++|+.+.-|.....-+.+.|++.++++|.+..+-. .++++.+.++ +.|.+|.++-... +. ..| .||
T Consensus 2 ~~i~ac~~G~a~s~laa~~L~~aa~~~g~~~~ve~~~~~g~~~~l~~~~i~----~Ad~vi~~~~~~~--~~-~rf~gk~ 74 (96)
T cd05569 2 VAVTACPTGIAHTYMAAEALEKAAKKLGWEIKVETQGSLGIENELTAEDIA----EADAVILAADVPV--DD-ERFAGKR 74 (96)
T ss_pred EEEEECCCchhHHHHHHHHHHHHHHHCCCeEEEEEecCcCccCcCCHHHHh----hCCEEEEecCCCC--ch-hhhCCCe
Confidence 57788888888888899999999999999866442 4455555544 4679999999883 33 333 356
Q ss_pred cc
Q 042576 229 LL 230 (313)
Q Consensus 229 vL 230 (313)
++
T Consensus 75 v~ 76 (96)
T cd05569 75 VY 76 (96)
T ss_pred EE
Confidence 54
No 129
>PRK00061 ribH 6,7-dimethyl-8-ribityllumazine synthase; Provisional
Probab=42.47 E-value=66 Score=28.12 Aligned_cols=86 Identities=20% Similarity=0.170 Sum_probs=56.6
Q ss_pred CCEEEEEEeCCCCCCcHHHHHHHHHHHHHcCC---cEEEEEeCCCC-----HHHHhcCcCCccEEEEecCC-Ccccc---
Q 042576 153 ARTWGIVLGTLGRQGNPRILERLQKRMEKKGF---DYVVIMMSEIS-----PARVALFEDSVDAWIQIACP-RLSID--- 220 (313)
Q Consensus 153 A~~~GIIvgTLg~Q~~~~ii~~l~~ll~~~Gk---k~y~i~v~ein-----p~KLanf~~~ID~fV~iaCP-rlsid--- 220 (313)
.-+||||.+..-..-.-.+++...+.|++.|. ...++.|--.. ..+|+.-. ++|++|-++|- |...+
T Consensus 12 ~~riaIV~s~~n~~i~~~l~~ga~~~l~~~gv~~~~i~v~~VPGa~EiP~a~~~l~~~~-~~DavIalG~VIrG~T~H~e 90 (154)
T PRK00061 12 GLRIGIVVARFNDFITDALLEGALDALKRHGVSEENIDVVRVPGAFEIPLAAKKLAESG-KYDAVIALGAVIRGETPHFD 90 (154)
T ss_pred CCEEEEEEecCcHHHHHHHHHHHHHHHHHcCCCccceEEEECCCHHHHHHHHHHHHHcC-CCCEEEEEeeEEcCCCchHH
Confidence 35899999876555555666677778888893 34444444222 24666655 69999999998 33322
Q ss_pred ------------ccCCCCCc----ccCHHHHHHHh
Q 042576 221 ------------WGDAFTKP----LLTPFEAEIAL 239 (313)
Q Consensus 221 ------------~~~~f~kP----vLTPyE~~vAL 239 (313)
=+-++.+| ||||.-.+-|+
T Consensus 91 ~V~~~v~~gl~~v~l~~~~PV~~GVLt~~~~eQa~ 125 (154)
T PRK00061 91 YVANEVAKGLADVSLETGVPVGFGVLTTDTIEQAI 125 (154)
T ss_pred HHHHHHHHHHHHHHhccCCCEEEEecCCCCHHHHH
Confidence 13357788 57777777666
No 130
>PRK10703 DNA-binding transcriptional repressor PurR; Provisional
Probab=42.38 E-value=2.9e+02 Score=25.73 Aligned_cols=163 Identities=16% Similarity=0.113 Sum_probs=79.3
Q ss_pred eEEEEe-c---cccHhHHHHHHHHHHhCCCeEEecCC--CCCCCccccCCCCCCCCCCCCCCeEEEecCCcccHHH-HHh
Q 042576 39 KLILAG-T---IQFASAIRAAKPELEKQGFKVMIPQS--KPLSAGEVLGCTAPKIPARESDFNLVFIADGRFHLEA-FMI 111 (313)
Q Consensus 39 ~i~Lv~-t---iQf~~~l~~~~~~L~~~g~~v~ipq~--~pls~GevLGCt~~~~~~~~~~d~iv~igdGrFHle~-~mi 111 (313)
.|+++. + .-|...++.+.+.+++.|+++++-.. .+-...+.+ ..... ..+|++++.+.. ...+. -.+
T Consensus 61 ~i~vi~~~~~~~~~~~~~~gi~~~~~~~g~~~~~~~~~~~~~~~~~~i---~~l~~--~~vdgiii~~~~-~~~~~~~~l 134 (341)
T PRK10703 61 SIGLLATSSEAPYFAEIIEAVEKNCYQKGYTLILCNAWNNLEKQRAYL---SMLAQ--KRVDGLLVMCSE-YPEPLLAML 134 (341)
T ss_pred eEEEEeCCCCCchHHHHHHHHHHHHHHCCCEEEEEeCCCCHHHHHHHH---HHHHH--cCCCEEEEecCC-CCHHHHHHH
Confidence 577654 2 23555567888899999998765211 010000111 00001 137888876542 22222 123
Q ss_pred hC-CCceEEEeCCCC--Cc-ccccccChHH--HHHHHHHHHHHHhhcCCEEEEEEeCCCCCCcHHHHHHHHHHHHHcCCc
Q 042576 112 SN-PGIKTFRYDPYL--GK-LFLEEYDNKG--MRETRKRAIEKAMKEARTWGIVLGTLGRQGNPRILERLQKRMEKKGFD 185 (313)
Q Consensus 112 ~n-p~~~~y~yDPys--~~-~~~e~~d~~~--~l~~R~~~I~kak~~A~~~GIIvgTLg~Q~~~~ii~~l~~ll~~~Gkk 185 (313)
.. ..+|++.+|-.. .. ......|... .+..+ .+++ + ..+++++|-|..+......-.+-.++-++++|.+
T Consensus 135 ~~~~~iPvV~~d~~~~~~~~~~~v~~d~~~~g~~a~~-~L~~--~-G~~~i~~i~~~~~~~~~~~R~~Gf~~~l~~~gi~ 210 (341)
T PRK10703 135 EEYRHIPMVVMDWGEAKADFTDAIIDNAFEGGYLAGR-YLIE--R-GHRDIGVIPGPLERNTGAGRLAGFMKAMEEANIK 210 (341)
T ss_pred HhcCCCCEEEEecccCCcCCCCeEEECcHHHHHHHHH-HHHH--C-CCCcEEEEeCCccccchHHHHHHHHHHHHHcCCC
Confidence 33 467888876321 11 1111223211 11111 1222 3 5578999877655444444456667788888876
Q ss_pred EEE--EEeCCCCHH----HH----hcCcCCccEEEEe
Q 042576 186 YVV--IMMSEISPA----RV----ALFEDSVDAWIQI 212 (313)
Q Consensus 186 ~y~--i~v~einp~----KL----anf~~~ID~fV~i 212 (313)
... +..+..+++ .+ ..-+ ++|+++..
T Consensus 211 ~~~~~~~~~~~~~~~~~~~~~~~l~~~~-~~~ai~~~ 246 (341)
T PRK10703 211 VPEEWIVQGDFEPESGYEAMQQILSQKH-RPTAVFCG 246 (341)
T ss_pred CChHHeEeCCCCHHHHHHHHHHHHhCCC-CCCEEEEC
Confidence 432 333444443 22 2223 58887743
No 131
>cd06304 PBP1_BmpA_like Periplasmic binding component of a family of basic membrane lipoproteins from Borrelia and various putative lipoproteins from other bacteria. Periplasmic binding component of a family of basic membrane lipoproteins from Borrelia and various putative lipoproteins from other bacteria. These outer membrane proteins include Med, a cell-surface localized protein regulating the competence transcription factor gene comK in Bacillus subtilis, and PnrA, a periplasmic purine nucleoside binding protein of an ATP-binding cassette (ABC) transport system in Treponema pallidum. All contain the type I periplasmic sugar-binding protein-like fold.
Probab=42.38 E-value=2.5e+02 Score=25.08 Aligned_cols=131 Identities=13% Similarity=0.033 Sum_probs=61.4
Q ss_pred ccHhHHHHHHHHHHhCCCeEEecCC-CCCCCccccCCCCCCCCCCCCCCeEEEecCCcccHHH-HHhh-CCCceEEEeCC
Q 042576 47 QFASAIRAAKPELEKQGFKVMIPQS-KPLSAGEVLGCTAPKIPARESDFNLVFIADGRFHLEA-FMIS-NPGIKTFRYDP 123 (313)
Q Consensus 47 Qf~~~l~~~~~~L~~~g~~v~ipq~-~pls~GevLGCt~~~~~~~~~~d~iv~igdGrFHle~-~mi~-np~~~~y~yDP 123 (313)
-|...++.+.+.+++.|+++++-.. .+-..-+.+. .+.. ..+|++++.+.. +...- -.+. .+.+|+...|-
T Consensus 15 f~~~l~~gi~~~~~~~gy~~~~~~~~~~~~~~~~~~----~l~~-~~vdgiii~~~~-~~~~~~~~~~~~~~ipvv~~~~ 88 (260)
T cd06304 15 FNQSAYEGLEKAEKELGVEVKYVESVEDADYEPNLR----QLAA-QGYDLIFGVGFG-FMDAVEKVAKEYPDVKFAIIDG 88 (260)
T ss_pred HHHHHHHHHHHHHHhcCceEEEEecCCHHHHHHHHH----HHHH-cCCCEEEECCcc-hhHHHHHHHHHCCCCEEEEecC
Confidence 4555567788888888888665211 1100001110 0000 136888776533 22111 1222 34678777764
Q ss_pred CC---CcccccccChHHHHHHHHH--HHHHHhhcCCEEEEEEeCCCCCCcHHHHHHHHHHHHHcCCcEE
Q 042576 124 YL---GKLFLEEYDNKGMRETRKR--AIEKAMKEARTWGIVLGTLGRQGNPRILERLQKRMEKKGFDYV 187 (313)
Q Consensus 124 ys---~~~~~e~~d~~~~l~~R~~--~I~kak~~A~~~GIIvgTLg~Q~~~~ii~~l~~ll~~~Gkk~y 187 (313)
.. ..+.....|. ...-+.. ++.+.. ..+++|+|.|... .....-++-.++.++++|....
T Consensus 89 ~~~~~~~~~~v~~d~--~~~~~~a~~l~~~~~-g~~~I~~i~~~~~-~~~~~R~~Gf~~~~~~~~~~~~ 153 (260)
T cd06304 89 VVDAPPNVASYVFRE--YEGSYLAGVLAALMT-KTGKVGFVGGMPI-PEVNRFINGFAAGAKSVNPDIT 153 (260)
T ss_pred ccCCCCCeeeeecch--HHHHHHHHHHHHHhc-cCCceEEEecccc-HHHHHHHHHHHHHHHHhCCCcE
Confidence 22 1111112232 2222222 222223 6689999987542 2222224445667888886543
No 132
>TIGR01752 flav_long flavodoxin, long chain. Flavodoxins are small redox-active proteins with a flavin mononucleotide (FMN) prosthetic group. They can act in nitrogen fixation by nitrogenase, in sulfite reduction, and light-dependent NADP+ reduction in during photosynthesis, among other roles. This model describes the long chain type, typical for nitrogen fixation but associated with pyruvate formate-lyase activation and cobalamin-dependent methionine synthase activity in E. coli.
Probab=42.26 E-value=59 Score=28.07 Aligned_cols=49 Identities=16% Similarity=0.213 Sum_probs=32.7
Q ss_pred ccCChHHHHHHHHHhCCCCCeEEEEec---c----ccHhHHHHHHHHHHhCCCeEE
Q 042576 19 IKIDVNRLIDTIKVNYSDPGKLILAGT---I----QFASAIRAAKPELEKQGFKVM 67 (313)
Q Consensus 19 i~iD~~~~i~~i~~~f~~~~~i~Lv~t---i----Qf~~~l~~~~~~L~~~g~~v~ 67 (313)
.+-+...+++.+...-..+++++++++ . .|..++..+.+.|++.|.+++
T Consensus 60 ~p~~~~~fl~~l~~~~l~gk~v~~fg~g~~~~y~~~f~~a~~~l~~~l~~~G~~~i 115 (167)
T TIGR01752 60 LQEDWEDFLPTLEELDFTGKTVALFGLGDQEGYSETFCDGMGILYDKIKARGAKVV 115 (167)
T ss_pred CcHHHHHHHHHhhcCCCCCCEEEEEecCCCCcccHHHHHHHHHHHHHHHHcCCeEE
Confidence 343455677776543234678998885 2 335568889999998888764
No 133
>cd06307 PBP1_uncharacterized_sugar_binding Periplasmic sugar-binding domain of uncharacterized transport systems. Periplasmic sugar-binding domain of uncharacterized transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein (PBP1) superfamily. The members of this group are predicted to be involved in the transport of sugar-containing molecules across cellular and organellar membranes.
Probab=42.10 E-value=39 Score=30.40 Aligned_cols=33 Identities=9% Similarity=-0.054 Sum_probs=18.5
Q ss_pred EEEEEeCCCCCCcHHHHHHHHHHHHHcCCcEEE
Q 042576 156 WGIVLGTLGRQGNPRILERLQKRMEKKGFDYVV 188 (313)
Q Consensus 156 ~GIIvgTLg~Q~~~~ii~~l~~ll~~~Gkk~y~ 188 (313)
+|+|+....-.....+++.+++.+++.|...++
T Consensus 2 ig~v~~~~~~~~~~~~~~~i~~~~~~~g~~~~~ 34 (275)
T cd06307 2 LGFLLPKGSNAFYRELAAALEAAAAAFPDARIR 34 (275)
T ss_pred eEEEeCCCCChHHHHHHHHHHHHHhhhhccCce
Confidence 566665555555555666666666665544333
No 134
>cd06285 PBP1_LacI_like_7 Ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. This group includes the ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.
Probab=42.09 E-value=2.5e+02 Score=24.87 Aligned_cols=131 Identities=10% Similarity=0.047 Sum_probs=64.0
Q ss_pred ccHhHHHHHHHHHHhCCCeEEecC--CCCCCCccccCCCCCCCCCCCCCCeEEEecCCcccHHHHHhhCCCceEEEeCCC
Q 042576 47 QFASAIRAAKPELEKQGFKVMIPQ--SKPLSAGEVLGCTAPKIPARESDFNLVFIADGRFHLEAFMISNPGIKTFRYDPY 124 (313)
Q Consensus 47 Qf~~~l~~~~~~L~~~g~~v~ipq--~~pls~GevLGCt~~~~~~~~~~d~iv~igdGrFHle~~mi~np~~~~y~yDPy 124 (313)
.|...++.+.+.+++.|+.+++-. ..+...-+.+. .... ..+|++++.+.......--.+..-.+|++.+|..
T Consensus 13 ~~~~~~~gi~~~~~~~~~~~~~~~~~~~~~~~~~~i~---~l~~--~~~dgiii~~~~~~~~~~~~~~~~~iPvv~~~~~ 87 (265)
T cd06285 13 VMATMYEGIEEAAAERGYSTFVANTGDNPDAQRRAIE---MLLD--RRVDGLILGDARSDDHFLDELTRRGVPFVLVLRH 87 (265)
T ss_pred cHHHHHHHHHHHHHHCCCEEEEEeCCCCHHHHHHHHH---HHHH--cCCCEEEEecCCCChHHHHHHHHcCCCEEEEccC
Confidence 455666778888888888765411 11100000000 0001 1367777665322222111123335788877754
Q ss_pred CCcccccccChHHH--HHHHHHHHHHHhhcCCEEEEEEeCCCCCCcHHHHHHHHHHHHHcCCcE
Q 042576 125 LGKLFLEEYDNKGM--RETRKRAIEKAMKEARTWGIVLGTLGRQGNPRILERLQKRMEKKGFDY 186 (313)
Q Consensus 125 s~~~~~e~~d~~~~--l~~R~~~I~kak~~A~~~GIIvgTLg~Q~~~~ii~~l~~ll~~~Gkk~ 186 (313)
.........|..+. ...++ + ..+ ..+++|+|.|..+......-++-.++-++++|.+.
T Consensus 88 ~~~~~~V~~d~~~ag~~a~~~-L--~~~-g~~~i~~i~~~~~~~~~~~R~~Gf~~~~~~~~~~~ 147 (265)
T cd06285 88 AGTSPAVTGDDVLGGRLATRH-L--LDL-GHRRIAVLAGPDYASTARDRLAGFRAALAEAGIEV 147 (265)
T ss_pred CCCCCEEEeCcHHHHHHHHHH-H--HHC-CCccEEEEeCCcccccHHHHHHHHHHHHHHcCCCC
Confidence 33222222332221 11111 1 123 56789999887665444455566677788888653
No 135
>cd06277 PBP1_LacI_like_1 Ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. This group includes the ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.
Probab=41.81 E-value=2.4e+02 Score=25.05 Aligned_cols=132 Identities=16% Similarity=0.102 Sum_probs=62.1
Q ss_pred ccHhHHHHHHHHHHhCCCeEEecCCCCCCCccccCCCCCCCCCCCCCCeEEEecCCcccHHHH-HhhCCCceEEEeCCCC
Q 042576 47 QFASAIRAAKPELEKQGFKVMIPQSKPLSAGEVLGCTAPKIPARESDFNLVFIADGRFHLEAF-MISNPGIKTFRYDPYL 125 (313)
Q Consensus 47 Qf~~~l~~~~~~L~~~g~~v~ipq~~pls~GevLGCt~~~~~~~~~~d~iv~igdGrFHle~~-mi~np~~~~y~yDPys 125 (313)
.|...++.+.+.+++.|+++.+-....-...+. ..-..... ..+|++++.+.. +...+ .+....+|+..+|...
T Consensus 16 ~~~~~~~~i~~~~~~~g~~~~~~~~~~~~~~~~-~~~~~l~~--~~vdgiii~~~~--~~~~~~~l~~~~ipvV~~~~~~ 90 (268)
T cd06277 16 FYSEIYRAIEEEAKKYGYNLILKFVSDEDEEEF-ELPSFLED--GKVDGIILLGGI--STEYIKEIKELGIPFVLVDHYI 90 (268)
T ss_pred cHHHHHHHHHHHHHHcCCEEEEEeCCCChHHHH-HHHHHHHH--CCCCEEEEeCCC--ChHHHHHHhhcCCCEEEEccCC
Confidence 466667778888888888866522111000010 00000011 137888876532 22111 1223467888887543
Q ss_pred Cc--ccccccChHHHHHHHHHHH-HHHhhcCCEEEEEEeCCCCCCcHHHHHHHHHHHHHcCCcE
Q 042576 126 GK--LFLEEYDNKGMRETRKRAI-EKAMKEARTWGIVLGTLGRQGNPRILERLQKRMEKKGFDY 186 (313)
Q Consensus 126 ~~--~~~e~~d~~~~l~~R~~~I-~kak~~A~~~GIIvgTLg~Q~~~~ii~~l~~ll~~~Gkk~ 186 (313)
.. +.....|..+. -|..+- ...+ ..+++++|-+.........-.+-..+-++++|.+.
T Consensus 91 ~~~~~~~V~~d~~~~--~~~a~~~l~~~-g~~~i~~i~~~~~~~~~~~R~~gf~~~~~~~~~~~ 151 (268)
T cd06277 91 PNEKADCVLTDNYSG--AYAATEYLIEK-GHRKIGFVGDPLYSPSFEERYEGYKKALLDHGIPF 151 (268)
T ss_pred CCCCCCEEEecchHH--HHHHHHHHHHC-CCCcEEEECCCCCCcchHHHHHHHHHHHHHcCCCC
Confidence 21 21122333221 121111 1123 55788888655443444444455667777777653
No 136
>cd06288 PBP1_sucrose_transcription_regulator Ligand-binding domain of DNA-binding regulatory proteins specific to sucrose that are members of the LacI-GalR family of bacterial transcription repressors. This group includes the ligand-binding domain of DNA-binding regulatory proteins specific to sucrose that are members of the LacI-GalR family of bacterial transcription repressors. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.
Probab=41.61 E-value=1e+02 Score=27.28 Aligned_cols=60 Identities=17% Similarity=0.144 Sum_probs=38.6
Q ss_pred EEEEEEeCC-CCCCcHHHHHHHHHHHHHcCCcEEEEEeCCCCHHH----HhcCc-CCccEEEEecCC
Q 042576 155 TWGIVLGTL-GRQGNPRILERLQKRMEKKGFDYVVIMMSEISPAR----VALFE-DSVDAWIQIACP 215 (313)
Q Consensus 155 ~~GIIvgTL-g~Q~~~~ii~~l~~ll~~~Gkk~y~i~v~einp~K----Lanf~-~~ID~fV~iaCP 215 (313)
+||+|+-.. .-.....+++.+++.+++.|....++. .+-++++ +.++. ..+|+.|+.++.
T Consensus 1 ~ig~v~~~~~~~~~~~~~~~~i~~~~~~~g~~~~~~~-~~~~~~~~~~~~~~l~~~~~dgiii~~~~ 66 (269)
T cd06288 1 TIGLISDEIATTPFAVEIILGAQDAAREHGYLLLVVN-TGGDDELEAEAVEALLDHRVDGIIYATMY 66 (269)
T ss_pred CeEEEeCCCCCCccHHHHHHHHHHHHHHCCCEEEEEe-CCCCHHHHHHHHHHHHHcCCCEEEEecCC
Confidence 478888776 556666788888888888887654443 3334432 22221 148888887763
No 137
>COG2185 Sbm Methylmalonyl-CoA mutase, C-terminal domain/subunit (cobalamin-binding) [Lipid metabolism]
Probab=41.45 E-value=59 Score=28.29 Aligned_cols=57 Identities=18% Similarity=0.293 Sum_probs=40.6
Q ss_pred HHHHHhhcCCEEEEEEeCCCCCCcHHHHHHHHHHHHHcCCcEEEEE-eCCCCHHHHhcCc
Q 042576 145 AIEKAMKEARTWGIVLGTLGRQGNPRILERLQKRMEKKGFDYVVIM-MSEISPARVALFE 203 (313)
Q Consensus 145 ~I~kak~~A~~~GIIvgTLg~Q~~~~ii~~l~~ll~~~Gkk~y~i~-v~einp~KLanf~ 203 (313)
++..|. +...=.|.++++. +++...+..+.+.|+++|.+-..++ =|.|.|+.+.+|.
T Consensus 55 ~v~aA~-~~dv~vIgvSsl~-g~h~~l~~~lve~lre~G~~~i~v~~GGvip~~d~~~l~ 112 (143)
T COG2185 55 AVRAAV-EEDVDVIGVSSLD-GGHLTLVPGLVEALREAGVEDILVVVGGVIPPGDYQELK 112 (143)
T ss_pred HHHHHH-hcCCCEEEEEecc-chHHHHHHHHHHHHHHhCCcceEEeecCccCchhHHHHH
Confidence 344453 3333445667765 7889999999999999999888844 4588888765554
No 138
>cd01537 PBP1_Repressors_Sugar_Binding_like Ligand-binding domain of the LacI-GalR family of transcription regulators and the sugar-binding domain of ABC-type transport systems. Ligand-binding domain of the LacI-GalR family of transcription regulators and the sugar-binding domain of ABC-type transport systems, all of which contain the type I periplasmic binding protein-like fold. Their specific ligands include lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars. The LacI family of proteins consists of transcriptional regulators related to the lac repressor; in general the sugar binding domain in this family binds a sugar, which in turn changes the DNA binding activity of the repressor domain. The core structure of the periplasmic binding proteins is classified into two types and they differ in number and order of beta strands in each domain: type I, which has six beta strands, and type II, which has five beta strands. These two distinct structural arrangem
Probab=41.35 E-value=83 Score=27.24 Aligned_cols=30 Identities=13% Similarity=0.360 Sum_probs=13.4
Q ss_pred EEEEEeCCCCCCcHHHHHHHHHHHHHcCCc
Q 042576 156 WGIVLGTLGRQGNPRILERLQKRMEKKGFD 185 (313)
Q Consensus 156 ~GIIvgTLg~Q~~~~ii~~l~~ll~~~Gkk 185 (313)
+|+++...+-.....+++-+++.+++.|.+
T Consensus 2 ig~v~~~~~~~~~~~~~~g~~~~~~~~g~~ 31 (264)
T cd01537 2 IGVLVPDLDNPFFAQVLKGIEEAAKAAGYQ 31 (264)
T ss_pred eEEEEcCCCChHHHHHHHHHHHHHHHcCCe
Confidence 444443333333344444455555554444
No 139
>cd06312 PBP1_ABC_sugar_binding_like_4 Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems. Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily, which consists of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis.
Probab=41.24 E-value=71 Score=28.65 Aligned_cols=60 Identities=12% Similarity=-0.020 Sum_probs=31.2
Q ss_pred EEEEEEeCC-CCCCcHHHHHHHHHHHHHcCCcEEEEEeCCCCHHHHhcC-----cCCccEEEEecC
Q 042576 155 TWGIVLGTL-GRQGNPRILERLQKRMEKKGFDYVVIMMSEISPARVALF-----EDSVDAWIQIAC 214 (313)
Q Consensus 155 ~~GIIvgTL-g~Q~~~~ii~~l~~ll~~~Gkk~y~i~v~einp~KLanf-----~~~ID~fV~iaC 214 (313)
+||+|+..+ .-.....+++.+++.+++.|....++....-++++.... ...+|++|+.++
T Consensus 1 ~i~~i~~~~~~~~~~~~~~~g~~~~~~~~g~~v~~~~~~~~~~~~~~~~i~~l~~~~vdgiii~~~ 66 (271)
T cd06312 1 KIAFVTHGPAGDPFWTVVKNGAEDAAKDLGVDVEYRGPETFDVADMARLIEAAIAAKPDGIVVTIP 66 (271)
T ss_pred CEEEecCCCCCCcHHHHHHHHHHHHHHHhCCEEEEECCCCCCHHHHHHHHHHHHHhCCCEEEEeCC
Confidence 356666554 445555666666666666665554443332244433211 113666666554
No 140
>cd05013 SIS_RpiR RpiR-like protein. RpiR contains a SIS (Sugar ISomerase) domain, which is found in many phosphosugar isomerases and phosphosugar binding proteins. In E. coli, rpiR negatively regulates the expression of rpiB gene. Both rpiB and rpiA are ribose phosphate isomerases that catalyze the reversible reactions of ribose 5-phosphate into ribulose 5-phosphate.
Probab=41.13 E-value=1.7e+02 Score=23.01 Aligned_cols=68 Identities=18% Similarity=0.195 Sum_probs=46.4
Q ss_pred HHHHHhhcCCEEEEEEeCCCCCCcHHHHHHHHHHHHHcCCcEEEEEeCCCCHHHHhcCcCCccEEEEecCCCcc
Q 042576 145 AIEKAMKEARTWGIVLGTLGRQGNPRILERLQKRMEKKGFDYVVIMMSEISPARVALFEDSVDAWIQIACPRLS 218 (313)
Q Consensus 145 ~I~kak~~A~~~GIIvgTLg~Q~~~~ii~~l~~ll~~~Gkk~y~i~v~einp~KLanf~~~ID~fV~iaCPrls 218 (313)
.++... +++++ +++|+ ..+..+.+.+...++..|+..+.+.-.+....-+.+.. +=|++|.++--+.+
T Consensus 6 ~~~~i~-~~~~i-~i~g~---g~s~~~a~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~i~iS~~g~~ 73 (139)
T cd05013 6 AVDLLA-KARRI-YIFGV---GSSGLVAEYLAYKLLRLGKPVVLLSDPHLQLMSAANLT-PGDVVIAISFSGET 73 (139)
T ss_pred HHHHHH-hCCEE-EEEEc---CchHHHHHHHHHHHHHcCCceEEecCHHHHHHHHHcCC-CCCEEEEEeCCCCC
Confidence 444555 67776 66666 45778999999999999998776644443333334455 56899988877653
No 141
>cd06286 PBP1_CcpB_like Ligand-binding domain of a novel transcription factor implicated in catabolite repression in Bacillus and Clostridium species. This group includes the ligand-binding domain of a novel transcription factor implicated in catabolite repression in Bacillus and Clostridium species. CcpB is 30% identical in sequence to CcpA which functions as the major transcriptional regulator of carbon catabolite repression/regulation (CCR), a process in which enzymes necessary for the metabolism of alternative sugars are inhibited in the presence of glucose. Like CcpA, the DNA-binding protein CcpB exerts its catabolite-repressing effect by a mechanism dependent on the presence of HPr(Ser-P), the small phosphocarrier proteins of the phosphoenolpyruvate-sugar phosphotransferase system, but with a less significant degree.
Probab=41.04 E-value=2.3e+02 Score=24.95 Aligned_cols=129 Identities=14% Similarity=0.133 Sum_probs=62.1
Q ss_pred cHhHHHHHHHHHHhCCCeEEecCC--CCCCCccccCCCCCCCCCCCCCCeEEEecCCcccHHHH-HhhCCCceEEEeCCC
Q 042576 48 FASAIRAAKPELEKQGFKVMIPQS--KPLSAGEVLGCTAPKIPARESDFNLVFIADGRFHLEAF-MISNPGIKTFRYDPY 124 (313)
Q Consensus 48 f~~~l~~~~~~L~~~g~~v~ipq~--~pls~GevLGCt~~~~~~~~~~d~iv~igdGrFHle~~-mi~np~~~~y~yDPy 124 (313)
|...++.+.+.+++.|+++++-.. .+-..-+++. .+.. ..+|+++..+... ....+ .+.. ..|++.+|-.
T Consensus 14 ~~~i~~gi~~~~~~~g~~~~~~~~~~~~~~~~~~i~----~l~~-~~vdgiii~~~~~-~~~~~~~~~~-~~pvv~~~~~ 86 (260)
T cd06286 14 FSQLVDGIEKAALKHGYKVVLLQTNYDKEKELEYLE----LLKT-KQVDGLILCSREN-DWEVIEPYTK-YGPIVLCEEY 86 (260)
T ss_pred HHHHHHHHHHHHHHcCCEEEEEeCCCChHHHHHHHH----HHHH-cCCCEEEEeCCCC-CHHHHHHHhc-CCCEEEEecc
Confidence 455567788888888888765221 1100001110 0000 2368877765321 11111 1222 2366666643
Q ss_pred CC-cccccccChHHHHHHHHHHHHHHh-hcCCEEEEEEeCCCCCCcHHHHHHHHHHHHHcCCcE
Q 042576 125 LG-KLFLEEYDNKGMRETRKRAIEKAM-KEARTWGIVLGTLGRQGNPRILERLQKRMEKKGFDY 186 (313)
Q Consensus 125 s~-~~~~e~~d~~~~l~~R~~~I~kak-~~A~~~GIIvgTLg~Q~~~~ii~~l~~ll~~~Gkk~ 186 (313)
.. .+.....|..+ .-|. +.+... ...+++|+|.|..+......-.+-.++-++++|.+.
T Consensus 87 ~~~~~~~v~~d~~~--~~~~-~~~~l~~~g~~~i~~i~~~~~~~~~~~R~~Gf~~~l~~~~~~~ 147 (260)
T cd06286 87 DSKNISSVYIDHYE--AFYE-ALKYLIQKGYRKIAYCIGRKKSLNSQSRKKAYKDALEEYGLTP 147 (260)
T ss_pred cCCCCCEEEECChH--HHHH-HHHHHHHCCCceEEEEcCCcccchhHHHHHHHHHHHHHcCCCC
Confidence 22 11112223222 1121 112111 156789999887655555566677778888888553
No 142
>TIGR01481 ccpA catabolite control protein A. Catabolite control protein A is a LacI family global transcriptional regulator found in Gram-positive bacteria. CcpA is involved in repressing carbohydrate utilization genes [ex: alpha-amylase (amyE), acetyl-coenzyme A synthase (acsA)] and in activating genes involved in transporting excess carbon from the cell [ex: acetate kinase (ackA), alpha-acetolactate synthase (alsS)]. Additionally, disruption of CcpA in Bacillus megaterium, Staphylococcus xylosus, Lactobacillus casei and Lactocacillus pentosus also decreases growth rate, which suggests CcpA is involved in the regulation of other metabolic pathways.
Probab=40.69 E-value=1.6e+02 Score=27.17 Aligned_cols=63 Identities=11% Similarity=0.208 Sum_probs=44.8
Q ss_pred cCCEEEEEEeCCCCCCcHHHHHHHHHHHHHcCCcEEEEEeCCCCHHHH----hcC-cCCccEEEEecCC
Q 042576 152 EARTWGIVLGTLGRQGNPRILERLQKRMEKKGFDYVVIMMSEISPARV----ALF-EDSVDAWIQIACP 215 (313)
Q Consensus 152 ~A~~~GIIvgTLg~Q~~~~ii~~l~~ll~~~Gkk~y~i~v~einp~KL----anf-~~~ID~fV~iaCP 215 (313)
..++||+++..+.-..+..+++.+++.++++|....+.. +.-++++. ..+ ...+|.+|++++.
T Consensus 58 ~~~~Igvv~~~~~~~f~~~l~~~i~~~~~~~g~~~~i~~-~~~~~~~~~~~~~~l~~~~vdGiIi~~~~ 125 (329)
T TIGR01481 58 RTTTVGVIIPDISNIYYAELARGIEDIATMYKYNIILSN-SDEDPEKEVQVLNTLLSKQVDGIIFMGGT 125 (329)
T ss_pred CCCEEEEEeCCCCchhHHHHHHHHHHHHHHcCCEEEEEe-CCCCHHHHHHHHHHHHhCCCCEEEEeCCC
Confidence 457999999988777888899999999999998765543 33344322 222 1259999988764
No 143
>TIGR00147 lipid kinase, YegS/Rv2252/BmrU family. The E. coli member of this family, YegS has been purified and shown to have phosphatidylglycerol kinase activity. The member from M. tuberculosis, Rv2252, has diacylglycerol kinase activity. BmrU from B. subtilis is in an operon with multidrug efflux transporter Bmr, but is uncharacterized.
Probab=40.44 E-value=1.2e+02 Score=28.22 Aligned_cols=40 Identities=15% Similarity=0.179 Sum_probs=25.4
Q ss_pred CEEEEEEeCCCCCCc-HHHHHHHHHHHHHcCCcEEEEEeCC
Q 042576 154 RTWGIVLGTLGRQGN-PRILERLQKRMEKKGFDYVVIMMSE 193 (313)
Q Consensus 154 ~~~GIIvgTLg~Q~~-~~ii~~l~~ll~~~Gkk~y~i~v~e 193 (313)
++++||+...++.+. .+.++++++.|+++|.++.++....
T Consensus 2 ~~~~ii~Np~sg~~~~~~~~~~i~~~l~~~~~~~~~~~t~~ 42 (293)
T TIGR00147 2 AEAPAILNPTAGKSNDNKPLREVIMLLREEGMEIHVRVTWE 42 (293)
T ss_pred ceEEEEECCCccchhhHHHHHHHHHHHHHCCCEEEEEEecC
Confidence 357777777665543 4566677777777777766555443
No 144
>PF03698 UPF0180: Uncharacterised protein family (UPF0180); InterPro: IPR005370 The members of this family are small uncharacterised proteins.
Probab=40.31 E-value=56 Score=25.65 Aligned_cols=40 Identities=13% Similarity=0.271 Sum_probs=27.3
Q ss_pred HhHHHHHHHHHHhCCCeEEecCCCCCCCccccCCCCCCCCCCCCCCeEEEecCCc
Q 042576 49 ASAIRAAKPELEKQGFKVMIPQSKPLSAGEVLGCTAPKIPARESDFNLVFIADGR 103 (313)
Q Consensus 49 ~~~l~~~~~~L~~~g~~v~ipq~~pls~GevLGCt~~~~~~~~~~d~iv~igdGr 103 (313)
...|..+++.|++.||+|+-... ...+ ..+||+|+-|.+.
T Consensus 7 E~~Ls~v~~~L~~~GyeVv~l~~------------~~~~---~~~daiVvtG~~~ 46 (80)
T PF03698_consen 7 EEGLSNVKEALREKGYEVVDLEN------------EQDL---QNVDAIVVTGQDT 46 (80)
T ss_pred cCCchHHHHHHHHCCCEEEecCC------------cccc---CCcCEEEEECCCc
Confidence 45678999999999999873211 0011 2479999888764
No 145
>cd06288 PBP1_sucrose_transcription_regulator Ligand-binding domain of DNA-binding regulatory proteins specific to sucrose that are members of the LacI-GalR family of bacterial transcription repressors. This group includes the ligand-binding domain of DNA-binding regulatory proteins specific to sucrose that are members of the LacI-GalR family of bacterial transcription repressors. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.
Probab=40.30 E-value=2.6e+02 Score=24.61 Aligned_cols=61 Identities=11% Similarity=0.111 Sum_probs=35.0
Q ss_pred cCCEEEEEEeCCCCCCcHHHHHHHHHHHHHcCCcE--EEEEeCCCCHH-------H-HhcCcCCccEEEEec
Q 042576 152 EARTWGIVLGTLGRQGNPRILERLQKRMEKKGFDY--VVIMMSEISPA-------R-VALFEDSVDAWIQIA 213 (313)
Q Consensus 152 ~A~~~GIIvgTLg~Q~~~~ii~~l~~ll~~~Gkk~--y~i~v~einp~-------K-Lanf~~~ID~fV~ia 213 (313)
.-+++++|-|..+......-.+-.++.++++|.+. ..+..+..+++ + |+.-+ ++|+++..+
T Consensus 115 g~~~i~~l~~~~~~~~~~~R~~gf~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~-~~~ai~~~~ 185 (269)
T cd06288 115 GHRRIAFINGEPWMLAAKDRLKGYRQALAEAGIPFDPDLVVHGDWSADDGYEAAAALLDLDD-RPTAIFCGN 185 (269)
T ss_pred CCceEEEEeCCccchhHHHHHHHHHHHHHHcCCCCCHHHeEeCCCChHHHHHHHHHHHhCCC-CCCEEEEeC
Confidence 45689998877654444445566677788888542 22334555532 1 22334 578776543
No 146
>COG0529 CysC Adenylylsulfate kinase and related kinases [Inorganic ion transport and metabolism]
Probab=39.94 E-value=73 Score=29.11 Aligned_cols=39 Identities=18% Similarity=0.275 Sum_probs=34.3
Q ss_pred cCCEEEEEEeCCCCCCcHHHHHHHHHHHHHcCCcEEEEE
Q 042576 152 EARTWGIVLGTLGRQGNPRILERLQKRMEKKGFDYVVIM 190 (313)
Q Consensus 152 ~A~~~GIIvgTLg~Q~~~~ii~~l~~ll~~~Gkk~y~i~ 190 (313)
..+-+-|-+.-|++.|--.|...|.+.|.++|+.+|++=
T Consensus 20 ~~~~~viW~TGLSGsGKSTiA~ale~~L~~~G~~~y~LD 58 (197)
T COG0529 20 GQKGAVIWFTGLSGSGKSTIANALEEKLFAKGYHVYLLD 58 (197)
T ss_pred CCCCeEEEeecCCCCCHHHHHHHHHHHHHHcCCeEEEec
Confidence 344567889999999999999999999999999999863
No 147
>cd06296 PBP1_CatR_like Ligand-binding domain of a LacI-like transcriptional regulator, CatR which is involved in catechol degradation. This group includes the ligand-binding domain of a LacI-like transcriptional regulator, CatR which is involved in catechol degradation. This group belongs to the the LacI-GalR family repressors that are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.
Probab=39.90 E-value=2.7e+02 Score=24.62 Aligned_cols=128 Identities=12% Similarity=0.130 Sum_probs=61.8
Q ss_pred cHhHHHHHHHHHHhCCCeEEecCCC--CCCCccccCCCCCCCCCCCCCCeEEEecCCcccHHHH-HhhCCCceEEEeCCC
Q 042576 48 FASAIRAAKPELEKQGFKVMIPQSK--PLSAGEVLGCTAPKIPARESDFNLVFIADGRFHLEAF-MISNPGIKTFRYDPY 124 (313)
Q Consensus 48 f~~~l~~~~~~L~~~g~~v~ipq~~--pls~GevLGCt~~~~~~~~~~d~iv~igdGrFHle~~-mi~np~~~~y~yDPy 124 (313)
|...++.+.+.+++.|+++++-... +...-+.+- .... ..+|++++.+... ....+ .+.....|++.+|-.
T Consensus 14 ~~~~~~gi~~~~~~~g~~~~~~~~~~~~~~~~~~i~---~l~~--~~~dgiii~~~~~-~~~~~~~~~~~~ipvV~i~~~ 87 (270)
T cd06296 14 ASEVLRGVEEAAAAAGYDVVLSESGRRTSPERQWVE---RLSA--RRTDGVILVTPEL-TSAQRAALRRTGIPFVVVDPA 87 (270)
T ss_pred HHHHHHHHHHHHHHcCCeEEEecCCCchHHHHHHHH---HHHH--cCCCEEEEecCCC-ChHHHHHHhcCCCCEEEEecc
Confidence 4455566777777778876542111 100000000 0001 1367777664321 11111 122345677777643
Q ss_pred C---CcccccccChH---HHHHHHHHHHHHHhhcCCEEEEEEeCCCCCCcHHHHHHHHHHHHHcCCcE
Q 042576 125 L---GKLFLEEYDNK---GMRETRKRAIEKAMKEARTWGIVLGTLGRQGNPRILERLQKRMEKKGFDY 186 (313)
Q Consensus 125 s---~~~~~e~~d~~---~~l~~R~~~I~kak~~A~~~GIIvgTLg~Q~~~~ii~~l~~ll~~~Gkk~ 186 (313)
. ..+.....|.. +...+ .+++ + ..+++++|.|..+-.....-.+-.++.++++|.+.
T Consensus 88 ~~~~~~~~~v~~d~~~~~~~a~~--~l~~--~-g~~~i~~i~~~~~~~~~~~r~~gf~~~~~~~~~~~ 150 (270)
T cd06296 88 GDPDADVPSVGATNWAGGLAATE--HLLE--L-GHRRIGFITGPPDLLCSRARLDGYRAALAEAGIPV 150 (270)
T ss_pred cCCCCCCCEEEeCcHHHHHHHHH--HHHH--c-CCCcEEEEcCCCcchhHHHHHHHHHHHHHHcCCCC
Confidence 2 11221223322 22211 1222 3 56789999887765555666677778888887653
No 148
>PF03358 FMN_red: NADPH-dependent FMN reductase; InterPro: IPR005025 NADPH-dependent FMN reductase (1.5.1.29 from EC) reduces FMN and also reduces riboflavin and FAD, although more slowly. Members of this entry catalyse the reaction NAD(P)H + FMN = NAD(P)(+) + FMNH(2).; PDB: 3SVL_B 3GFS_F 3GFQ_A 1NNI_1 2GSW_B 3GFR_D 1T0I_B 3D7N_A 2R97_A 3B6K_A ....
Probab=39.79 E-value=63 Score=26.82 Aligned_cols=40 Identities=18% Similarity=0.329 Sum_probs=34.0
Q ss_pred EEEEEEeCCCCCC-cHHHHHHHHHHHHHcCCcEEEEEeCCC
Q 042576 155 TWGIVLGTLGRQG-NPRILERLQKRMEKKGFDYVVIMMSEI 194 (313)
Q Consensus 155 ~~GIIvgTLg~Q~-~~~ii~~l~~ll~~~Gkk~y~i~v~ei 194 (313)
+|.||.|+....+ +..+++.+.+.+++.|.++-+|-+.+.
T Consensus 2 kilii~gS~r~~~~t~~l~~~~~~~l~~~g~e~~~i~l~~~ 42 (152)
T PF03358_consen 2 KILIINGSPRKNSNTRKLAEAVAEQLEEAGAEVEVIDLADY 42 (152)
T ss_dssp EEEEEESSSSTTSHHHHHHHHHHHHHHHTTEEEEEEECTTS
T ss_pred EEEEEECcCCCCCHHHHHHHHHHHHHHHcCCEEEEEecccc
Confidence 5789999985444 456999999999999999999999986
No 149
>cd01541 PBP1_AraR Ligand-binding domain of DNA transcription repressor specific for arabinose (AraR) which is a member of the LacI-GalR family of bacterial transcription regulators. Ligand-binding domain of DNA transcription repressor specific for arabinose (AraR) which is a member of the LacI-GalR family of bacterial transcription regulators. The ligand-binding domain of AraR is structurally homologous to the periplasmic sugar-binding domain of ABC-type transporters and both domains contain the type I periplasmic binding protein-like fold. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the type I periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which i
Probab=39.67 E-value=1.1e+02 Score=27.42 Aligned_cols=31 Identities=16% Similarity=0.389 Sum_probs=16.5
Q ss_pred EEEEEeCCCCCCcHHHHHHHHHHHHHcCCcE
Q 042576 156 WGIVLGTLGRQGNPRILERLQKRMEKKGFDY 186 (313)
Q Consensus 156 ~GIIvgTLg~Q~~~~ii~~l~~ll~~~Gkk~ 186 (313)
||+++.++..-....+++.+++.++++|...
T Consensus 2 igvv~~~~~~~~~~~~~~gi~~~~~~~g~~~ 32 (273)
T cd01541 2 IGVITTYISDYIFPSIIRGIESVLSEKGYSL 32 (273)
T ss_pred eEEEeCCccchhHHHHHHHHHHHHHHcCCEE
Confidence 4555555554445555555555555555444
No 150
>PRK06455 riboflavin synthase; Provisional
Probab=39.57 E-value=1.1e+02 Score=26.94 Aligned_cols=58 Identities=16% Similarity=0.158 Sum_probs=40.5
Q ss_pred CEEEEEEeCCCCCCcHHHHHHHHHHHHHcC--CcEEEEEeCCCC-----HHHHhcCcCCccEEEEecCC
Q 042576 154 RTWGIVLGTLGRQGNPRILERLQKRMEKKG--FDYVVIMMSEIS-----PARVALFEDSVDAWIQIACP 215 (313)
Q Consensus 154 ~~~GIIvgTLg~Q~~~~ii~~l~~ll~~~G--kk~y~i~v~ein-----p~KLanf~~~ID~fV~iaCP 215 (313)
.+||||.+|..+. .+.+-..+.|+++| .+..++.|--.. ..+|+.=. .+|++|-++|+
T Consensus 2 ~kigIV~s~fn~~---~L~~gAi~~L~~~g~~~~I~v~~VPGa~ELP~aakkL~~~~-~yDaVIaLG~V 66 (155)
T PRK06455 2 MKIGIADTTFARV---DMGSAAIDELRKLDPSAKIIRYTVPGIKDLPVAAKKLIEEE-GCDIVMALGMP 66 (155)
T ss_pred cEEEEEEEecchH---HHHHHHHHHHHhcCCCCceEEEECCCHHHHHHHHHHHHhcC-CCCEEEEecce
Confidence 4799999998875 56777788888855 455555444322 23555434 69999999998
No 151
>cd06304 PBP1_BmpA_like Periplasmic binding component of a family of basic membrane lipoproteins from Borrelia and various putative lipoproteins from other bacteria. Periplasmic binding component of a family of basic membrane lipoproteins from Borrelia and various putative lipoproteins from other bacteria. These outer membrane proteins include Med, a cell-surface localized protein regulating the competence transcription factor gene comK in Bacillus subtilis, and PnrA, a periplasmic purine nucleoside binding protein of an ATP-binding cassette (ABC) transport system in Treponema pallidum. All contain the type I periplasmic sugar-binding protein-like fold.
Probab=39.27 E-value=78 Score=28.46 Aligned_cols=34 Identities=18% Similarity=0.138 Sum_probs=20.1
Q ss_pred EEEEEEeC--CCCCCcHHHHHHHHHHHHHcCCcEEE
Q 042576 155 TWGIVLGT--LGRQGNPRILERLQKRMEKKGFDYVV 188 (313)
Q Consensus 155 ~~GIIvgT--Lg~Q~~~~ii~~l~~ll~~~Gkk~y~ 188 (313)
+||+|+.. +.-..+..+++.+++.+++.|....+
T Consensus 1 ~Igvi~~~~~~~~~f~~~l~~gi~~~~~~~gy~~~~ 36 (260)
T cd06304 1 KVALVYDGGGGDKSFNQSAYEGLEKAEKELGVEVKY 36 (260)
T ss_pred CEEEEecCCCCcchHHHHHHHHHHHHHHhcCceEEE
Confidence 36666653 44455556666677766666655433
No 152
>cd06320 PBP1_allose_binding Periplasmic allose-binding domain of bacterial transport systems that function as a primary receptor of active transport and chemotaxis. Periplasmic allose-binding domain of bacterial transport systems that function as a primary receptor of active transport and chemotaxis. The members of this group are belonging to a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily. Like other periplasmic receptors of the ABC-type transport systems, the allose-binding protein consists of two alpha/beta domains connected by a three-stranded hinge. This Venus flytrap-like domain undergoes transition from an open to a closed conformational state upon ligand binding.
Probab=39.24 E-value=58 Score=29.20 Aligned_cols=30 Identities=27% Similarity=0.380 Sum_probs=14.6
Q ss_pred EEEEEeCCCCCCcHHHHHHHHHHHHHcCCc
Q 042576 156 WGIVLGTLGRQGNPRILERLQKRMEKKGFD 185 (313)
Q Consensus 156 ~GIIvgTLg~Q~~~~ii~~l~~ll~~~Gkk 185 (313)
+|+|+..+..-....+++.+++.++++|..
T Consensus 2 igvi~~~~~~~~~~~~~~gi~~~~~~~g~~ 31 (275)
T cd06320 2 YGVVLKTLSNEFWRSLKEGYENEAKKLGVS 31 (275)
T ss_pred eeEEEecCCCHHHHHHHHHHHHHHHHhCCe
Confidence 455554444334444555555555555544
No 153
>cd06299 PBP1_LacI_like_13 Ligand-binding domain of DNA-binding regulatory protein from Corynebacterium glutamicum which has a unique ability to produce significant amounts of L-glutamate directly from cheap sugar and ammonia. This group includes the ligand-binding domain of DNA-binding regulatory protein from Corynebacterium glutamicum which has a unique ability to produce significant amounts of L-glutamate directly from cheap sugar and ammonia. This regulatory protein is a member of the LacI-GalR family of bacterial transcription repressors. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial trans
Probab=39.23 E-value=2.7e+02 Score=24.50 Aligned_cols=64 Identities=13% Similarity=0.175 Sum_probs=36.2
Q ss_pred cCCEEEEEEeCCCCCCcHHHHHHHHHHHHHcCCc--EEEEEeCCCCHH----HHhc-CcCCccEEEEecCC
Q 042576 152 EARTWGIVLGTLGRQGNPRILERLQKRMEKKGFD--YVVIMMSEISPA----RVAL-FEDSVDAWIQIACP 215 (313)
Q Consensus 152 ~A~~~GIIvgTLg~Q~~~~ii~~l~~ll~~~Gkk--~y~i~v~einp~----KLan-f~~~ID~fV~iaCP 215 (313)
..+++++|.|+........-.+-.++-++++|.+ ...+..+..+++ .+.. |...+|+++-.++.
T Consensus 115 g~~~I~~i~~~~~~~~~~~R~~gf~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~av~~~~d~ 185 (265)
T cd06299 115 GHKKIGYISGPQDTSTGRERLEAFRQACASLGLEVNEDLVVLGGYSQESGYAGATKLLDQGATAIIAGDSM 185 (265)
T ss_pred CCCcEEEEeCCCCcccHHHHHHHHHHHHHHCCCCCChHhEEecCcchHHHHHHHHHHHcCCCCEEEEcCcH
Confidence 4578999988876544445556677888888843 223334444432 1222 22126766655543
No 154
>PRK10310 PTS system galactitol-specific transporter subunit IIB; Provisional
Probab=39.08 E-value=1e+02 Score=24.36 Aligned_cols=53 Identities=13% Similarity=0.084 Sum_probs=34.5
Q ss_pred EEEeCCCCCCcHHHHHHHHHHHHHcCCcEEEEEeCCCCHHHHhcCcCCccEEEEec
Q 042576 158 IVLGTLGRQGNPRILERLQKRMEKKGFDYVVIMMSEISPARVALFEDSVDAWIQIA 213 (313)
Q Consensus 158 IIvgTLg~Q~~~~ii~~l~~ll~~~Gkk~y~i~v~einp~KLanf~~~ID~fV~ia 213 (313)
++++.-|..-+.-+..++++.++++|..+-+.- .+...+.+..+++|++|.+.
T Consensus 6 LvvCgsG~~TS~m~~~ki~~~l~~~gi~~~v~~---~~~~e~~~~~~~~D~iv~t~ 58 (94)
T PRK10310 6 IVACGGAVATSTMAAEEIKELCQSHNIPVELIQ---CRVNEIETYMDGVHLICTTA 58 (94)
T ss_pred EEECCCchhHHHHHHHHHHHHHHHCCCeEEEEE---ecHHHHhhhcCCCCEEEECC
Confidence 456665655555568999999999999865444 33333443322689887665
No 155
>cd06318 PBP1_ABC_sugar_binding_like_9 Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems. Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily, which consists of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis.
Probab=39.05 E-value=62 Score=29.06 Aligned_cols=60 Identities=13% Similarity=0.088 Sum_probs=35.5
Q ss_pred EEEEEEeCCCCCCcHHHHHHHHHHHHHcCCcEEEEEeCCCCHHH----HhcCc-CCccEEEEecCC
Q 042576 155 TWGIVLGTLGRQGNPRILERLQKRMEKKGFDYVVIMMSEISPAR----VALFE-DSVDAWIQIACP 215 (313)
Q Consensus 155 ~~GIIvgTLg~Q~~~~ii~~l~~ll~~~Gkk~y~i~v~einp~K----Lanf~-~~ID~fV~iaCP 215 (313)
++|+|+.++.......+++.+++.+++.|.+..+.. +.-++++ |..+- ..+|++|+.++-
T Consensus 1 ~igv~~~~~~~~~~~~~~~~i~~~~~~~g~~v~~~~-~~~~~~~~~~~i~~~~~~~~Dgiii~~~~ 65 (282)
T cd06318 1 KIGFSQYTLNSPFFAALTEAAKAHAKALGYELISTD-AQGDLTKQIADVEDLLTRGVNVLIINPVD 65 (282)
T ss_pred CeeEEeccccCHHHHHHHHHHHHHHHHcCCEEEEEc-CCCCHHHHHHHHHHHHHcCCCEEEEecCC
Confidence 467777777666666777788888887776654332 2334432 22221 137777776653
No 156
>PF01583 APS_kinase: Adenylylsulphate kinase; InterPro: IPR002891 Protein phosphorylation, which plays a key role in most cellular activities, is a reversible process mediated by protein kinases and phosphoprotein phosphatases. Protein kinases catalyse the transfer of the gamma phosphate from nucleotide triphosphates (often ATP) to one or more amino acid residues in a protein substrate side chain, resulting in a conformational change affecting protein function. Phosphoprotein phosphatases catalyse the reverse process. Protein kinases fall into three broad classes, characterised with respect to substrate specificity []: Serine/threonine-protein kinases Tyrosine-protein kinases Dual specific protein kinases (e.g. MEK - phosphorylates both Thr and Tyr on target proteins) Protein kinase function has been evolutionarily conserved from Escherichia coli to human []. Protein kinases play a role in a multitude of cellular processes, including division, proliferation, apoptosis, and differentiation []. Phosphorylation usually results in a functional change of the target protein by changing enzyme activity, cellular location, or association with other proteins. The catalytic subunits of protein kinases are highly conserved, and several structures have been solved [], leading to large screens to develop kinase-specific inhibitors for the treatments of a number of diseases []. This domain contains an ATP binding P-loop motif [].; GO: 0005524 ATP binding, 0016301 kinase activity, 0016772 transferase activity, transferring phosphorus-containing groups, 0000103 sulfate assimilation; PDB: 1M7H_B 1M7G_B 3CR7_B 1D6J_A 2OFW_G 1X6V_B 1XNJ_A 1XJQ_B 2PEY_A 2PEZ_B ....
Probab=39.03 E-value=72 Score=27.92 Aligned_cols=36 Identities=19% Similarity=0.317 Sum_probs=31.3
Q ss_pred EEEEEeCCCCCCcHHHHHHHHHHHHHcCCcEEEEEe
Q 042576 156 WGIVLGTLGRQGNPRILERLQKRMEKKGFDYVVIMM 191 (313)
Q Consensus 156 ~GIIvgTLg~Q~~~~ii~~l~~ll~~~Gkk~y~i~v 191 (313)
+-|.+.-|++.|--.+...|.+.|.+.|+++|++=.
T Consensus 3 ~vIwltGlsGsGKtTlA~~L~~~L~~~g~~~~~LDg 38 (156)
T PF01583_consen 3 FVIWLTGLSGSGKTTLARALERRLFARGIKVYLLDG 38 (156)
T ss_dssp EEEEEESSTTSSHHHHHHHHHHHHHHTTS-EEEEEH
T ss_pred EEEEEECCCCCCHHHHHHHHHHHHHHcCCcEEEecC
Confidence 457888899999999999999999999999999843
No 157
>cd06295 PBP1_CelR Ligand binding domain of a transcription regulator of cellulose genes, CelR, which is highly homologous to the LacI-GalR family of bacterial transcription regulators. This group includes the ligand binding domain of a transcription regulator of cellulose genes, CelR, which is highly homologous to the LacI-GalR family of bacterial transcription regulators. The binding of CelR to the celE promoter is inhibited specifically by cellobiose. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn chang
Probab=38.61 E-value=2.9e+02 Score=24.61 Aligned_cols=155 Identities=11% Similarity=0.129 Sum_probs=71.3
Q ss_pred cHhHHHHHHHHHHhCCCeEEecCCCCCCCccccCCCCCCCCCCCCCCeEEEecCCcccHHHHH-hhCCCceEEEeCCCCC
Q 042576 48 FASAIRAAKPELEKQGFKVMIPQSKPLSAGEVLGCTAPKIPARESDFNLVFIADGRFHLEAFM-ISNPGIKTFRYDPYLG 126 (313)
Q Consensus 48 f~~~l~~~~~~L~~~g~~v~ipq~~pls~GevLGCt~~~~~~~~~~d~iv~igdGrFHle~~m-i~np~~~~y~yDPys~ 126 (313)
|...++.+.+.+++.|+++.+-.......-+++ ..+.. ..+|++|+.+... ....+- +...++|++.+|-...
T Consensus 25 ~~~~~~gi~~~~~~~g~~~~v~~~~~~~~~~~~----~~l~~-~~~dgiii~~~~~-~~~~~~~~~~~~ipvV~~~~~~~ 98 (275)
T cd06295 25 FLSLLGGIADALAERGYDLLLSFVSSPDRDWLA----RYLAS-GRADGVILIGQHD-QDPLPERLAETGLPFVVWGRPLP 98 (275)
T ss_pred HHHHHHHHHHHHHHcCCEEEEEeCCchhHHHHH----HHHHh-CCCCEEEEeCCCC-ChHHHHHHHhCCCCEEEECCccC
Confidence 444566677778888887654211110000010 00101 2368887765422 111111 2334678887774322
Q ss_pred --cccccccChH---HHHHHHHHHHHHHhhcCCEEEEEEeCCCCCCcHHHHHHHHHHHHHcCCcEE--EEEeCCCCHH--
Q 042576 127 --KLFLEEYDNK---GMRETRKRAIEKAMKEARTWGIVLGTLGRQGNPRILERLQKRMEKKGFDYV--VIMMSEISPA-- 197 (313)
Q Consensus 127 --~~~~e~~d~~---~~l~~R~~~I~kak~~A~~~GIIvgTLg~Q~~~~ii~~l~~ll~~~Gkk~y--~i~v~einp~-- 197 (313)
.+.....|.. ++.... ++ .+ ..+.+++|.+.........-.+-.++-++++|.... .+..+.-+.+
T Consensus 99 ~~~~~~V~~d~~~~g~~~a~~--l~--~~-g~~~i~~i~~~~~~~~~~~r~~gf~~~~~~~~~~~~~~~~~~~~~~~~~~ 173 (275)
T cd06295 99 GQPYCYVGSDNVGGGRLATEH--LL--AR-GRRRIAFLGGPQDMPEGEERLEGYREALAEAGLPLDPRLVAPGDFTEESG 173 (275)
T ss_pred CCCCCEEEECcHHHHHHHHHH--HH--HC-CCCeEEEEcCCCCcchhHHHHHHHHHHHHHcCCCCChhhEEeccCCHHHH
Confidence 1222223322 222221 22 23 567898887655423333445566777777774321 1222332322
Q ss_pred --H----HhcCcCCccEEEEecC
Q 042576 198 --R----VALFEDSVDAWIQIAC 214 (313)
Q Consensus 198 --K----Lanf~~~ID~fV~iaC 214 (313)
. |..-+ ++|+++....
T Consensus 174 ~~~~~~~l~~~~-~~~ai~~~~~ 195 (275)
T cd06295 174 RAAMRALLERGP-DFDAVFAASD 195 (275)
T ss_pred HHHHHHHHhCCC-CCCEEEECCc
Confidence 2 22334 5888776653
No 158
>cd06289 PBP1_MalI_like Ligand-binding domain of MalI, a transcription regulator of the maltose system of Escherichia coli and its close homologs from other bacteria. This group includes the ligand-binding domain of MalI, a transcription regulator of the maltose system of Escherichia coli and its close homologs from other bacteria. They are members of the LacI-GalR family of repressor proteins which are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.
Probab=38.37 E-value=2.8e+02 Score=24.36 Aligned_cols=33 Identities=12% Similarity=0.163 Sum_probs=23.7
Q ss_pred cCCEEEEEEeCCCCCCcHHHHHHHHHHHHHcCC
Q 042576 152 EARTWGIVLGTLGRQGNPRILERLQKRMEKKGF 184 (313)
Q Consensus 152 ~A~~~GIIvgTLg~Q~~~~ii~~l~~ll~~~Gk 184 (313)
..+++|++.|...........+-.++.++++|.
T Consensus 116 g~~~i~~l~~~~~~~~~~~r~~gf~~~l~~~~~ 148 (268)
T cd06289 116 GHRRIAFIGGLEDSSTRRERLAGYRAALAEAGL 148 (268)
T ss_pred CCCCEEEecCCccccchHHHHHHHHHHHHHcCC
Confidence 557899888776554555666777888888874
No 159
>cd01540 PBP1_arabinose_binding Periplasmic L-arabinose-binding protein (ABP), a member of a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily. Periplasmic L-arabinose-binding protein (ABP), a member of a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily. ABP is only involved in transport contrary to other related sugar-binding proteins such as the glucose/galactose-binding protein (GGBP) and the ribose-binding protein (RBP), both of which are involved in chemotaxis as well as transport. The periplasmic ABP consists of two alpha/beta globular domains connected by a three-stranded hinge, a Venus flytrap-like domain, which undergoes a transition from an open to a closed conformational state upon ligand binding. Moreover, ABP is homologous to the ligand-binding domain of eukaryotic receptors such as metabotropic glutamate receptor (mGluR) and DNA-binding transcriptional repressors such a
Probab=38.30 E-value=69 Score=28.93 Aligned_cols=58 Identities=14% Similarity=0.120 Sum_probs=31.3
Q ss_pred EEEEEEeCCCCCCcHHHHHHHHHHHHHcCCcEEEEEeCCCCHHHHh----cCc-CCccEEEEecC
Q 042576 155 TWGIVLGTLGRQGNPRILERLQKRMEKKGFDYVVIMMSEISPARVA----LFE-DSVDAWIQIAC 214 (313)
Q Consensus 155 ~~GIIvgTLg~Q~~~~ii~~l~~ll~~~Gkk~y~i~v~einp~KLa----nf~-~~ID~fV~iaC 214 (313)
+||+|+.++.-.....+++.+++.+++.|.+..++ -+. ++++.. ++. ..+|++|+.++
T Consensus 1 ~Ig~v~~~~~~~~~~~~~~gi~~~~~~~g~~~~~~-~~~-~~~~~~~~i~~~~~~~~dgiii~~~ 63 (289)
T cd01540 1 KIGFIVKQPEEPWFQTEWKFAKKAAKEKGFTVVKI-DVP-DGEKVLSAIDNLGAQGAKGFVICVP 63 (289)
T ss_pred CeeeecCCCCCcHHHHHHHHHHHHHHHcCCEEEEc-cCC-CHHHHHHHHHHHHHcCCCEEEEccC
Confidence 36677766655566666777777777766553322 222 443322 111 13677766654
No 160
>cd04502 SGNH_hydrolase_like_7 Members of the SGNH-hydrolase superfamily, a diverse family of lipases and esterases. The tertiary fold of the enzyme is substantially different from that of the alpha/beta hydrolase family and unique among all known hydrolases; its active site closely resembles the Ser-His-Asp(Glu) triad from other serine hydrolases, but may lack the carboxlic acid.
Probab=37.77 E-value=94 Score=26.12 Aligned_cols=24 Identities=8% Similarity=-0.104 Sum_probs=15.0
Q ss_pred HHHHHHHHHHHhhcCCEEEEEEeCC
Q 042576 139 RETRKRAIEKAMKEARTWGIVLGTL 163 (313)
Q Consensus 139 l~~R~~~I~kak~~A~~~GIIvgTL 163 (313)
+..|......+. ....+-|.+||-
T Consensus 38 ~~~~~~~~~~~~-~p~~vvi~~G~N 61 (171)
T cd04502 38 CLHYFDRLVLPY-QPRRVVLYAGDN 61 (171)
T ss_pred HHHHHHhhhccC-CCCEEEEEEecC
Confidence 444544444455 677888888883
No 161
>PRK08662 nicotinate phosphoribosyltransferase; Reviewed
Probab=37.69 E-value=69 Score=31.55 Aligned_cols=56 Identities=20% Similarity=0.350 Sum_probs=41.6
Q ss_pred CEEEEEEeCCCC--CCcHHHHHHHHHHHHHcC-CcEEEEEeCCCCHHHHhcCcCCccEE
Q 042576 154 RTWGIVLGTLGR--QGNPRILERLQKRMEKKG-FDYVVIMMSEISPARVALFEDSVDAW 209 (313)
Q Consensus 154 ~~~GIIvgTLg~--Q~~~~ii~~l~~ll~~~G-kk~y~i~v~einp~KLanf~~~ID~f 209 (313)
+..||.+=+.+- ..-.+.++++++.+++.| .+..+.+.|.||+++++.|...||+|
T Consensus 227 ~~d~I~LDn~~~~~g~l~~~v~~vr~~ld~~g~~~v~IeaSGgI~~~ni~~ya~~vD~i 285 (343)
T PRK08662 227 RLDGVRLDTPSSRRGNFRKIVREVRWTLDIRGYEHVKIFVSGGLDPERIRELRDVVDGF 285 (343)
T ss_pred cCCEEEcCCCCCCCccHHHHHHHHHHHHHhcCCCCeEEEEeCCCCHHHHHHHHHhCCEE
Confidence 456777777663 445567778888888887 45778888999999999997336665
No 162
>PRK06756 flavodoxin; Provisional
Probab=37.68 E-value=98 Score=25.80 Aligned_cols=47 Identities=17% Similarity=0.253 Sum_probs=32.2
Q ss_pred ChHHHHHHHHHhCCCCCeEEEEecc-----ccHhHHHHHHHHHHhCCCeEEe
Q 042576 22 DVNRLIDTIKVNYSDPGKLILAGTI-----QFASAIRAAKPELEKQGFKVMI 68 (313)
Q Consensus 22 D~~~~i~~i~~~f~~~~~i~Lv~ti-----Qf~~~l~~~~~~L~~~g~~v~i 68 (313)
+...+++.+...-..++++++++|- .|-.++..+.+.|++.|.+++.
T Consensus 68 ~~~~fl~~l~~~~l~~k~~~~fgt~~~~y~~~~~a~~~l~~~l~~~g~~~v~ 119 (148)
T PRK06756 68 DFLDFYDAMDSIDLTGKKAAVFGSCDSAYPKYGVAVDILIEKLQERGAAVVL 119 (148)
T ss_pred HHHHHHHHHhcCCCCCCEEEEEeCCCCchHHHHHHHHHHHHHHHHCCCEEcC
Confidence 3566777665322246678888762 2457788899999998888653
No 163
>cd02071 MM_CoA_mut_B12_BD methylmalonyl CoA mutase B12 binding domain. This domain binds to B12 (adenosylcobamide), which initiates the conversion of succinyl CoA and methylmalonyl CoA by forming an adenosyl radical, which then undergoes a rearrangement exchanging a hydrogen atom with a group attached to a neighboring carbon atom. This family is present in both mammals and bacteria. Bacterial members are heterodimers and involved in the fermentation of pyruvate to propionate. Mammalian members are homodimers and responsible for the conversion of odd-chain fatty acids and branched-chain amino acids via propionyl CoA to succinyl CoA for further degradation.
Probab=37.58 E-value=1.6e+02 Score=24.05 Aligned_cols=62 Identities=15% Similarity=0.208 Sum_probs=39.6
Q ss_pred cCCEEEEEEeCCCCCCcHHHHHHHHHHHHHcCCcE-EEEEeCCCCHHHHhcCc-CCccEEEEecCCC
Q 042576 152 EARTWGIVLGTLGRQGNPRILERLQKRMEKKGFDY-VVIMMSEISPARVALFE-DSVDAWIQIACPR 216 (313)
Q Consensus 152 ~A~~~GIIvgTLg~Q~~~~ii~~l~~ll~~~Gkk~-y~i~v~einp~KLanf~-~~ID~fV~iaCPr 216 (313)
++..++| +.+ ...+...++.+.+.|++.|... .+++-|...++..+.|. -.+|.|+-.+|+-
T Consensus 50 ~~d~V~i--S~~-~~~~~~~~~~~~~~L~~~~~~~i~i~~GG~~~~~~~~~~~~~G~d~~~~~~~~~ 113 (122)
T cd02071 50 DVDVIGL--SSL-SGGHMTLFPEVIELLRELGAGDILVVGGGIIPPEDYELLKEMGVAEIFGPGTSI 113 (122)
T ss_pred CCCEEEE--ccc-chhhHHHHHHHHHHHHhcCCCCCEEEEECCCCHHHHHHHHHCCCCEEECCCCCH
Confidence 4555554 444 3567777889999999998744 44455556565544321 1399998877763
No 164
>cd06308 PBP1_sensor_kinase_like Periplasmic binding domain of two-component sensor kinase signaling systems. Periplasmic binding domain of two-component sensor kinase signaling systems, some of which are fused with a C-terminal histidine kinase A domain (HisK) and/or a signal receiver domain (REC). Members of this group share homology with a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily and are predicted to be involved in sensing of environmental stimuli; their substrate specificities, however, are not known in detail.
Probab=37.42 E-value=95 Score=27.75 Aligned_cols=34 Identities=9% Similarity=0.200 Sum_probs=21.3
Q ss_pred EEEEEEeCCCCCCcHHHHHHHHHHHHHc-CCcEEE
Q 042576 155 TWGIVLGTLGRQGNPRILERLQKRMEKK-GFDYVV 188 (313)
Q Consensus 155 ~~GIIvgTLg~Q~~~~ii~~l~~ll~~~-Gkk~y~ 188 (313)
++|+|++++.-.....+++.+++.+++. |+...+
T Consensus 1 ~ig~~~~~~~~~~~~~~~~~i~~~~~~~~g~~~~~ 35 (270)
T cd06308 1 VIGFSQCNLADPWRAAMNDEIQREASNYPDVELII 35 (270)
T ss_pred CEEEEeeCCCCHHHHHHHHHHHHHHHhcCCcEEEE
Confidence 3677777665555566777777777764 555443
No 165
>PRK12359 flavodoxin FldB; Provisional
Probab=37.35 E-value=1.2e+02 Score=26.90 Aligned_cols=53 Identities=13% Similarity=0.197 Sum_probs=37.5
Q ss_pred EEEEEEeCCCCCCcHHHHHHHHHHHHHcCC-cEEEEEeCCCCHHHHhcCcCCccEEEEecCCC
Q 042576 155 TWGIVLGTLGRQGNPRILERLQKRMEKKGF-DYVVIMMSEISPARVALFEDSVDAWIQIACPR 216 (313)
Q Consensus 155 ~~GIIvgTLg~Q~~~~ii~~l~~ll~~~Gk-k~y~i~v~einp~KLanf~~~ID~fV~iaCPr 216 (313)
+++|+-+|.++ +...++++|.+.+ |. .+-++-+.+..++.|.++ | +|+++||=
T Consensus 2 ki~I~Y~S~TG-NTe~vAe~I~~~l---g~~~v~v~~i~~~~~~~l~~y----D-~iIlG~pT 55 (172)
T PRK12359 2 KIGLFYGSSTC-YTEMAAEKIRDII---GEELVDLHNLKDDPPKLMEQY----D-VLILGIPT 55 (172)
T ss_pred eEEEEEECCCC-HHHHHHHHHHHHh---CCCeEEEEEcccCChhHHccC----C-EEEEEecc
Confidence 57899999753 4556888888776 33 356677788887766655 4 57788886
No 166
>PF02012 BNR: BNR/Asp-box repeat; InterPro: IPR002860 Members of this entry contain multiple BNR (bacterial neuraminidase repeat) repeats or Asp-boxes. The repeats are short, however the repeats are never found closer than 40 residues together suggesting that the repeat is structurally longer. These repeats are found in a variety of non-homologous proteins, including bacterial ribonucleases, sulphite oxidases, reelin, netrins, sialidases, neuraminidases, some lipoprotein receptors, and a variety of glycosyl hydrolases [].; PDB: 2JKB_A 2VW0_A 2VW2_A 2VW1_A 2CN2_D 2CN3_B 2VK7_B 2VK5_A 2VK6_A 2BF6_A ....
Probab=37.29 E-value=18 Score=18.61 Aligned_cols=10 Identities=60% Similarity=1.647 Sum_probs=6.7
Q ss_pred eeccCCC-CCc
Q 042576 282 YYAQDGG-EWN 291 (313)
Q Consensus 282 ~y~~~~g-~w~ 291 (313)
|||.|+| -|+
T Consensus 1 ~~S~D~G~TW~ 11 (12)
T PF02012_consen 1 YYSTDGGKTWK 11 (12)
T ss_dssp EEESSTTSS-E
T ss_pred CEeCCCcccCc
Confidence 7888875 674
No 167
>COG1797 CobB Cobyrinic acid a,c-diamide synthase [Coenzyme metabolism]
Probab=37.17 E-value=1.5e+02 Score=30.57 Aligned_cols=75 Identities=17% Similarity=0.249 Sum_probs=49.7
Q ss_pred cccCChHHHHHHHHHhC--CC------------CCeEEEEeccccHhHHHHHHHHHHhCCCeEEecCCCCCCCccccCCC
Q 042576 18 EIKIDVNRLIDTIKVNY--SD------------PGKLILAGTIQFASAIRAAKPELEKQGFKVMIPQSKPLSAGEVLGCT 83 (313)
Q Consensus 18 ~i~iD~~~~i~~i~~~f--~~------------~~~i~Lv~tiQf~~~l~~~~~~L~~~g~~v~ipq~~pls~GevLGCt 83 (313)
+-.+|++.+++...+.. +. ..||++..|-.|.=..++..+.|++.|.+++. -+||...++
T Consensus 212 ~~~vDld~l~~ia~~~~~~~~~~~~~~~~~~~~~~rIAVA~D~AF~FyY~~nl~~Lr~~GAelv~--FSPL~D~~l---- 285 (451)
T COG1797 212 EKHVDLDALLEIASSAGPLEPDLSPEPERGNPLGVRIAVARDAAFNFYYPENLELLREAGAELVF--FSPLADEEL---- 285 (451)
T ss_pred HhhCCHHHHHHHHhccCCCCCCccccccccCCcCceEEEEecchhccccHHHHHHHHHCCCEEEE--eCCcCCCCC----
Confidence 34567777766665421 11 24799999999999999999999999999753 123322221
Q ss_pred CCCCCCCCCCCeEEEecCCccc
Q 042576 84 APKIPARESDFNLVFIADGRFH 105 (313)
Q Consensus 84 ~~~~~~~~~~d~iv~igdGrFH 105 (313)
+. ++|+ +|+|+|..-
T Consensus 286 ----P~--~~D~-vYlgGGYPE 300 (451)
T COG1797 286 ----PP--DVDA-VYLGGGYPE 300 (451)
T ss_pred ----CC--CCCE-EEeCCCChH
Confidence 22 2566 789999643
No 168
>cd01543 PBP1_XylR Ligand-binding domain of DNA transcription repressor specific for xylose (XylR). Ligand-binding domain of DNA transcription repressor specific for xylose (XylR), a member of the LacI-GalR family of bacterial transcription regulators. The ligand-binding domain of XylR is structurally homologous to the periplasmic sugar-binding domain of ABC-type transporters and both domains contain the type I periplasmic binding protein-like fold. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the type I periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.
Probab=37.11 E-value=59 Score=29.06 Aligned_cols=56 Identities=7% Similarity=0.021 Sum_probs=28.6
Q ss_pred EEEEEEeCCCCCCcHHHHHHHHHHHHH-cCCcEEEEEeCCCCHHHHhcCc-CCccEEEEec
Q 042576 155 TWGIVLGTLGRQGNPRILERLQKRMEK-KGFDYVVIMMSEISPARVALFE-DSVDAWIQIA 213 (313)
Q Consensus 155 ~~GIIvgTLg~Q~~~~ii~~l~~ll~~-~Gkk~y~i~v~einp~KLanf~-~~ID~fV~ia 213 (313)
+||+|+.+ .--.+..+++.+++.+++ .|....+.. +. ..+-+..+. ..+|.+|+..
T Consensus 1 ~ig~i~~~-~~~~~~~~~~gi~~~~~~~~g~~~~~~~-~~-~~~~~~~l~~~~vdGiI~~~ 58 (265)
T cd01543 1 RVALLVET-SSSYGRGVLRGIARYAREHGPWSIYLEP-RG-LQEPLRWLKDWQGDGIIARI 58 (265)
T ss_pred CeEEEecc-cchhhHHHHHHHHHHHHhcCCeEEEEec-cc-chhhhhhccccccceEEEEC
Confidence 36777763 345556677777777777 444433221 11 122222221 1377777654
No 169
>PRK10727 DNA-binding transcriptional regulator GalR; Provisional
Probab=37.03 E-value=2.1e+02 Score=26.86 Aligned_cols=62 Identities=11% Similarity=0.103 Sum_probs=43.8
Q ss_pred cCCEEEEEEeCCCCCCcHHHHHHHHHHHHHcCCcEEEEEeCCCCHHH----HhcC-cCCccEEEEecC
Q 042576 152 EARTWGIVLGTLGRQGNPRILERLQKRMEKKGFDYVVIMMSEISPAR----VALF-EDSVDAWIQIAC 214 (313)
Q Consensus 152 ~A~~~GIIvgTLg~Q~~~~ii~~l~~ll~~~Gkk~y~i~v~einp~K----Lanf-~~~ID~fV~iaC 214 (313)
..+++|+|+.++.-..+..+++.+++.++++|....+. -+.-++++ +.++ ...+|..|+.+.
T Consensus 58 ~~~~Igvi~~~~~~~f~~~~~~gi~~~~~~~g~~~~~~-~~~~~~~~~~~~i~~l~~~~vdgiIi~~~ 124 (343)
T PRK10727 58 STETVGLVVGDVSDPFFGAMVKAVEQVAYHTGNFLLIG-NGYHNEQKERQAIEQLIRHRCAALVVHAK 124 (343)
T ss_pred CCCeEEEEeCCCCcchHHHHHHHHHHHHHHcCCEEEEE-eCCCCHHHHHHHHHHHHhcCCCEEEEecC
Confidence 46789999998887888899999999999999764332 23334432 2232 124999998765
No 170
>PF00781 DAGK_cat: Diacylglycerol kinase catalytic domain; InterPro: IPR001206 The DAG-kinase catalytic domain or DAGKc domain is present in mammalian lipid kinases, such as diacylglycerol (DAG), ceramide and sphingosine kinases, as well as in related bacterial proteins [, ]. Eukaryotic DAG-kinase (2.7.1.107 from EC) catalyses the phosphorylation of DAG to phosphatidic acid, thus modulating the balance between the two signaling lipids. At least ten different isoforms have been identified in mammals, which form 5 groups characterised by different functional domains, such as the calcium-binding EF hand (see PDOC00018 from PROSITEDOC), PH (see PDOC50003 from PROSITEDOC), SAM (see PDOC50105 from PROSITEDOC) , DAG/PE-binding C1 domain (see PDOC00379 from PROSITEDOC) and ankyrin repeats (see PDOC50088 from PROSITEDOC) []. In bacteria, an integral membrane DAG kinase forms a homotrimeric protein that lacks the DAGKc domain (see PDOC00820 from PROSITEDOC). In contrast, the bacterial yegS protein is a soluble cytosolic protein that contains the DAGKc domain in the N-terminal part. YegS is a lipid kinase with two structural domains, wherein the active site is located in the interdomain cleft, C-terminal to the DAGKc domain which forms an alpha/beta fold []. The tertiary structure resembles that of NAD kinases and contains a metal-binding site in the C-terminal region [, ]. This domain is usually associated with an accessory domain (see IPR000756 from INTERPRO).; GO: 0004143 diacylglycerol kinase activity, 0007205 activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway; PDB: 2JGR_A 2BON_A 3T5P_D 3S40_A 2P1R_A 2QV7_A 2QVL_A.
Probab=36.84 E-value=1.2e+02 Score=24.71 Aligned_cols=40 Identities=15% Similarity=0.332 Sum_probs=32.4
Q ss_pred EEEEEEeCCCCCCcHHHHHHHHHHHHHcCCcEEEEEeCCCC
Q 042576 155 TWGIVLGTLGRQGNPRILERLQKRMEKKGFDYVVIMMSEIS 195 (313)
Q Consensus 155 ~~GIIvgTLg~Q~~~~ii~~l~~ll~~~Gkk~y~i~v~ein 195 (313)
++.||++.+++.+.-. ++++++.+++.+..+-++....-.
T Consensus 1 k~~vi~Np~sG~~~~~-~~~v~~~l~~~~~~~~~~~t~~~~ 40 (130)
T PF00781_consen 1 KVLVIINPKSGGGRAK-WKKVEPALRAAGIDYEVIETESAG 40 (130)
T ss_dssp SEEEEEETTSTTSHHH-HHHHHHHHHHTTCEEEEEEESSTT
T ss_pred CEEEEECCCCCCCchh-HHHHHHHHHHcCCceEEEEEeccc
Confidence 3678999999999999 799999999999887666665533
No 171
>PF02302 PTS_IIB: PTS system, Lactose/Cellobiose specific IIB subunit; InterPro: IPR003501 The bacterial phosphoenolpyruvate: sugar phosphotransferase system (PTS) is a multi-protein system involved in the regulation of a variety of metabolic and transcriptional processes. The lactose/cellobiose-specific family are one of four structurally and functionally distinct group IIB PTS system cytoplasmic enzymes. The fold of IIB cellobiose shows similar structure to mammalian tyrosine phosphatases. This signature is often found downstream of IPR003352 from INTERPRO.; GO: 0008982 protein-N(PI)-phosphohistidine-sugar phosphotransferase activity, 0009401 phosphoenolpyruvate-dependent sugar phosphotransferase system; PDB: 1TVM_A 2WY2_D 1IIB_A 2WWV_D 1H9C_A 1E2B_A 2L2Q_A 2KYR_A 3CZC_A 3NBM_A ....
Probab=36.65 E-value=1.3e+02 Score=22.71 Aligned_cols=55 Identities=18% Similarity=0.328 Sum_probs=34.3
Q ss_pred EEEeCCCCCCcHHHH-HHHHHHHHHcCCcEEEEEeCCCCHHHHhcCcCCccEEEEecCCCcc
Q 042576 158 IVLGTLGRQGNPRIL-ERLQKRMEKKGFDYVVIMMSEISPARVALFEDSVDAWIQIACPRLS 218 (313)
Q Consensus 158 IIvgTLg~Q~~~~ii-~~l~~ll~~~Gkk~y~i~v~einp~KLanf~~~ID~fV~iaCPrls 218 (313)
++++.-| -++--++ ++|++.+++.|.+...........+...+ ++|+++.. |.+.
T Consensus 3 lvvC~~G-i~TS~~~~~~i~~~~~~~gi~~~~~~~~~~~~~~~~~---~~D~il~~--~~i~ 58 (90)
T PF02302_consen 3 LVVCGSG-IGTSLMVANKIKKALKELGIEVEVSAGSILEVEEIAD---DADLILLT--PQIA 58 (90)
T ss_dssp EEEESSS-SHHHHHHHHHHHHHHHHTTECEEEEEEETTTHHHHHT---T-SEEEEE--ESSG
T ss_pred EEECCCh-HHHHHHHHHHHHHHHHhccCceEEEEecccccccccC---CCcEEEEc--Cccc
Confidence 3444444 4444455 99999999999888888887444333222 47877554 4444
No 172
>PRK06756 flavodoxin; Provisional
Probab=36.64 E-value=1.5e+02 Score=24.70 Aligned_cols=55 Identities=7% Similarity=0.154 Sum_probs=37.0
Q ss_pred EEEEEEeCCCCCCcHHHHHHHHHHHHHcCCcEEEEEeCCC-CHHHHhcCcCCccEEEEecCC
Q 042576 155 TWGIVLGTLGRQGNPRILERLQKRMEKKGFDYVVIMMSEI-SPARVALFEDSVDAWIQIACP 215 (313)
Q Consensus 155 ~~GIIvgTLg~Q~~~~ii~~l~~ll~~~Gkk~y~i~v~ei-np~KLanf~~~ID~fV~iaCP 215 (313)
++.||-+|. --+...+++.|.+.|++.|.++-++-+.+. .... +. +.|++ +++||
T Consensus 3 kv~IiY~S~-tGnTe~vA~~ia~~l~~~g~~v~~~~~~~~~~~~~---~~-~~d~v-i~gsp 58 (148)
T PRK06756 3 KLVMIFASM-SGNTEEMADHIAGVIRETENEIEVIDIMDSPEASI---LE-QYDGI-ILGAY 58 (148)
T ss_pred eEEEEEECC-CchHHHHHHHHHHHHhhcCCeEEEeehhccCCHHH---Hh-cCCeE-EEEeC
Confidence 577888884 344556899999999999988877766554 2333 33 35665 44554
No 173
>cd06300 PBP1_ABC_sugar_binding_like_1 Periplasmic sugar-binding component of uncharacterized ABC-type transport systems that are members of the pentose/hexose sugar-binding protein family of the type I periplasmic binding protein superfamily. Periplasmic sugar-binding component of uncharacterized ABC-type transport systems that are members of the pentose/hexose sugar-binding protein family of the type I periplasmic binding protein superfamily, which consists of two alpha/beta globular domains connected by a three-stranded hinge. This Venus flytrap-like domain undergoes transition from an open to a closed conformational state upon ligand binding. Members of this group are predicted to be involved in the transport of sugar-containing molecules across cellular and organellar membranes; however their substrate specificity is not known in detail.
Probab=36.23 E-value=1e+02 Score=27.47 Aligned_cols=60 Identities=15% Similarity=0.174 Sum_probs=31.7
Q ss_pred EEEEEEeCCCCCCcHHHHHHHHHHHHHc---CCcE-EEEEeCCCCHHHHhcC-----cCCccEEEEecC
Q 042576 155 TWGIVLGTLGRQGNPRILERLQKRMEKK---GFDY-VVIMMSEISPARVALF-----EDSVDAWIQIAC 214 (313)
Q Consensus 155 ~~GIIvgTLg~Q~~~~ii~~l~~ll~~~---Gkk~-y~i~v~einp~KLanf-----~~~ID~fV~iaC 214 (313)
+||+|+.....-.+..+++.+++.+++. |.+. .++.-+.-++++.... ...+|++|..++
T Consensus 1 ~Ig~i~~~~~~~~~~~~~~~i~~~~~~~~~~g~~~~l~i~~~~~~~~~~~~~~~~~~~~~vdgiIi~~~ 69 (272)
T cd06300 1 KIGLSNSYAGNTWRAQMLDEFKAQAKELKKAGLISEFIVTSADGDVAQQIADIRNLIAQGVDAIIINPA 69 (272)
T ss_pred CeEEeccccCChHHHHHHHHHHHHHHhhhccCCeeEEEEecCCCCHHHHHHHHHHHHHcCCCEEEEeCC
Confidence 3667776665555666777777777666 6543 2222333344432211 113677666554
No 174
>PRK08105 flavodoxin; Provisional
Probab=36.07 E-value=95 Score=26.46 Aligned_cols=41 Identities=20% Similarity=0.272 Sum_probs=33.1
Q ss_pred CEEEEEEeCCCCCCcHHHHHHHHHHHHHcCCcEEEEEeCCCC
Q 042576 154 RTWGIVLGTLGRQGNPRILERLQKRMEKKGFDYVVIMMSEIS 195 (313)
Q Consensus 154 ~~~GIIvgTLg~Q~~~~ii~~l~~ll~~~Gkk~y~i~v~ein 195 (313)
++++|+.||-++ +...++++|.+.|++.|.++.++-++.+.
T Consensus 2 ~~i~I~YgS~tG-nte~~A~~l~~~l~~~g~~~~~~~~~~~~ 42 (149)
T PRK08105 2 AKVGIFVGTVYG-NALLVAEEAEAILTAQGHEVTLFEDPELS 42 (149)
T ss_pred CeEEEEEEcCch-HHHHHHHHHHHHHHhCCCceEEechhhCC
Confidence 468999999753 34569999999999999998888776654
No 175
>cd06271 PBP1_AglR_RafR_like Ligand-binding domain of DNA transcription repressors specific for raffinose (RafR) and alpha-glucosides (AglR) which are members of the LacI-GalR family of bacterial transcription regulators. Ligand-binding domain of DNA transcription repressors specific for raffinose (RafR) and alpha-glucosides (AglR) which are members of the LacI-GalR family of bacterial transcription regulators. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the represso
Probab=35.92 E-value=3e+02 Score=24.10 Aligned_cols=159 Identities=10% Similarity=0.124 Sum_probs=73.3
Q ss_pred cccHhHHHHHHHHHHhCCCeEEecCCCCCCCccccCCCCCC-CCCCCCCCeEEEecCCcccHHHHHhhCCCceEEEeCCC
Q 042576 46 IQFASAIRAAKPELEKQGFKVMIPQSKPLSAGEVLGCTAPK-IPARESDFNLVFIADGRFHLEAFMISNPGIKTFRYDPY 124 (313)
Q Consensus 46 iQf~~~l~~~~~~L~~~g~~v~ipq~~pls~GevLGCt~~~-~~~~~~~d~iv~igdGrFHle~~mi~np~~~~y~yDPy 124 (313)
-.|...++.+.+.+++.|+++.+-....... +. .- ... +.. ..+|+++..+...-...--.+....+|++.+|-.
T Consensus 16 ~~~~~~~~~i~~~~~~~g~~~~~~~~~~~~~-~~-~~-~~~~~~~-~~vdgiii~~~~~~~~~~~~~~~~~ipvV~~~~~ 91 (268)
T cd06271 16 PFFAEFLSGLSEALAEHGYDLVLLPVDPDED-PL-EV-YRRLVES-GLVDGVIISRTRPDDPRVALLLERGFPFVTHGRT 91 (268)
T ss_pred ccHHHHHHHHHHHHHHCCceEEEecCCCcHH-HH-HH-HHHHHHc-CCCCEEEEecCCCCChHHHHHHhcCCCEEEECCc
Confidence 3455556777788888888765532211000 00 00 000 011 1367777654321111101122346677777622
Q ss_pred C--CcccccccChHHHHHHHHHHHHH--HhhcCCEEEEEEeCCCCCCcHHHHHHHHHHHHHcCCcE--EEEEeCCCCHHH
Q 042576 125 L--GKLFLEEYDNKGMRETRKRAIEK--AMKEARTWGIVLGTLGRQGNPRILERLQKRMEKKGFDY--VVIMMSEISPAR 198 (313)
Q Consensus 125 s--~~~~~e~~d~~~~l~~R~~~I~k--ak~~A~~~GIIvgTLg~Q~~~~ii~~l~~ll~~~Gkk~--y~i~v~einp~K 198 (313)
. ........|.... -+. +.+. .+ ..+++++|.|.........-.+-.++-++++|.+. ..+..+..+.++
T Consensus 92 ~~~~~~~~V~~d~~~~--~~~-a~~~l~~~-g~~~i~~i~~~~~~~~~~~R~~gf~~~~~~~~~~~~~~~~~~~~~~~~~ 167 (268)
T cd06271 92 ELGDPHPWVDFDNEAA--AYQ-AVRRLIAL-GHRRIALLNPPEDLTFAQHRRAGYRRALAEAGLPLDPALIVSGDMTEEG 167 (268)
T ss_pred CCCCCCCeEeeCcHHH--HHH-HHHHHHHc-CCCcEEEecCccccchHHHHHHHHHHHHHHhCCCCCCceEEeCCCChHH
Confidence 1 1121112232211 111 1111 13 56789998877654444445666778888887652 234445555432
Q ss_pred --------HhcCcCCccEEEEec
Q 042576 199 --------VALFEDSVDAWIQIA 213 (313)
Q Consensus 199 --------Lanf~~~ID~fV~ia 213 (313)
|...+ .+|+++..+
T Consensus 168 ~~~~~~~~l~~~~-~~~ai~~~~ 189 (268)
T cd06271 168 GYAAAAELLALPD-RPTAIVCSS 189 (268)
T ss_pred HHHHHHHHHhCCC-CCCEEEEcC
Confidence 22223 477776544
No 176
>PLN02349 glycerol-3-phosphate acyltransferase
Probab=35.17 E-value=89 Score=31.74 Aligned_cols=153 Identities=16% Similarity=0.154 Sum_probs=73.7
Q ss_pred cCChHHHHHHHHHhCCCCCeEEEEeccccHhHHHHHHHHHHhCCCeEEe-cCCCCCCCccc----cCCCCCCCCCCCCCC
Q 042576 20 KIDVNRLIDTIKVNYSDPGKLILAGTIQFASAIRAAKPELEKQGFKVMI-PQSKPLSAGEV----LGCTAPKIPARESDF 94 (313)
Q Consensus 20 ~iD~~~~i~~i~~~f~~~~~i~Lv~tiQf~~~l~~~~~~L~~~g~~v~i-pq~~pls~Gev----LGCt~~~~~~~~~~d 94 (313)
++|.-.|-......+-+.++ +.+-+.+.+.++.+.|.. |.+|++ ...-.-..-+| |.++.|.+. .
T Consensus 162 pfDyY~fg~~yirpLiDf~~----S~v~~~~~~~~i~e~l~~-g~nVvllsNHQseaDp~ii~llle~~~p~ia-----e 231 (426)
T PLN02349 162 PFDYYMFGQNYIRPLIDFRN----SYLGNRSRFDKVEEQLQQ-GHNVVLLSNHQSEADPAVIALLLEKSHPYLA-----E 231 (426)
T ss_pred cccHHHHHHHHHHHHhhccc----ceecCHHHHHHHHHHHhc-CCCEEEEeccccccchHHHHHHHhccCHHHH-----h
Confidence 45655444444333222222 334578889999999885 677765 22111111123 455555542 4
Q ss_pred eEEEecCCcccHHHHHhhCCC-ceEEEeCCCCCcccccccChHHHHHH--H---HHHHHHHhhcCCEEEEEE---eCCCC
Q 042576 95 NLVFIADGRFHLEAFMISNPG-IKTFRYDPYLGKLFLEEYDNKGMRET--R---KRAIEKAMKEARTWGIVL---GTLGR 165 (313)
Q Consensus 95 ~iv~igdGrFHle~~mi~np~-~~~y~yDPys~~~~~e~~d~~~~l~~--R---~~~I~kak~~A~~~GIIv---gTLg~ 165 (313)
.++||++.|--..-+ +.|. .---..+-|||+-.....+...+.++ . ..+..+.+ +.+.+ |.| |+..|
T Consensus 232 ~~iyvAGdrv~~DpL--~~PFSmGrNLlCVySKKhm~d~Pelke~K~~~N~kslk~~~~lL~-~Gg~~-iwIaPsGgRdR 307 (426)
T PLN02349 232 NVTYVAGDRVVTDPL--CKPFSMGRNLICVHSKKHMNDDPELKEMKRKANTRTLKEMALLLR-EGGQL-IWIAPSGGRDR 307 (426)
T ss_pred hhhhhccceEeeccc--cCccccCCceEEEEeccccCCChhhHHHHHHHHHHHHHHHHHHHh-cCCeE-EEEeCCCCCCC
Confidence 478887766321110 1111 00123344566544332222222111 1 22333445 43333 333 33333
Q ss_pred CCc-----------HHHHHHHHHHHHHcCCcE
Q 042576 166 QGN-----------PRILERLQKRMEKKGFDY 186 (313)
Q Consensus 166 Q~~-----------~~ii~~l~~ll~~~Gkk~ 186 (313)
..- +..++.++.+.+..|++.
T Consensus 308 ~d~~~g~~~papFD~~svd~mR~l~~~s~~pt 339 (426)
T PLN02349 308 PDPLTGEWTPAPFDPSAVDNMRRLTEKSKAPG 339 (426)
T ss_pred CCccCCCccCCCCChHHHHHHHHHHHhcCCCc
Confidence 333 567999999999998874
No 177
>cd02042 ParA ParA and ParB of Caulobacter crescentus belong to a conserved family of bacterial proteins implicated in chromosome segregation. ParB binds to DNA sequences adjacent to the origin of replication and localizes to opposite cell poles shortly following the initiation of DNA replication. ParB regulates the ParA ATPase activity by promoting nucleotide exchange in a fashion reminiscent of the exchange factors of eukaryotic G proteins. ADP-bound ParA binds single-stranded DNA, whereas the ATP-bound form dissociates ParB from its DNA binding sites. Increasing the fraction of ParA-ADP in the cell inhibits cell division, suggesting that this simple nucleotide switch may regulate cytokinesis. ParA shares sequence similarity to a conserved and widespread family of ATPases which includes the repA protein of the repABC operon in R. etli Sym plasmid. This operon is involved in the plasmid replication and partition.
Probab=35.08 E-value=1.4e+02 Score=22.84 Aligned_cols=48 Identities=21% Similarity=0.348 Sum_probs=38.6
Q ss_pred EEEeCCCCCCcHHHHHHHHHHHHHcCCcEEEEEeCCCCHHHHhcCcCCccEEEEecCCCc
Q 042576 158 IVLGTLGRQGNPRILERLQKRMEKKGFDYVVIMMSEISPARVALFEDSVDAWIQIACPRL 217 (313)
Q Consensus 158 IIvgTLg~Q~~~~ii~~l~~ll~~~Gkk~y~i~v~einp~KLanf~~~ID~fV~iaCPrl 217 (313)
.+.|.+|+-|...+...|-..+.++|++..++-++.- | | ||++-||..
T Consensus 3 ~~~~~kgG~Gkst~~~~la~~~~~~~~~vl~~d~d~~-------~----d-~viiD~p~~ 50 (104)
T cd02042 3 AVANQKGGVGKTTTAVNLAAALARRGKRVLLIDLDPQ-------Y----D-YIIIDTPPS 50 (104)
T ss_pred EEEeCCCCcCHHHHHHHHHHHHHhCCCcEEEEeCCCC-------C----C-EEEEeCcCC
Confidence 4678899999999999999999999998777665533 3 2 788888874
No 178
>PRK10401 DNA-binding transcriptional regulator GalS; Provisional
Probab=34.53 E-value=2.3e+02 Score=26.59 Aligned_cols=62 Identities=10% Similarity=0.030 Sum_probs=43.1
Q ss_pred cCCEEEEEEeCCCCCCcHHHHHHHHHHHHHcCCcEEEEEeCCCCHHHH----hcC-cCCccEEEEecC
Q 042576 152 EARTWGIVLGTLGRQGNPRILERLQKRMEKKGFDYVVIMMSEISPARV----ALF-EDSVDAWIQIAC 214 (313)
Q Consensus 152 ~A~~~GIIvgTLg~Q~~~~ii~~l~~ll~~~Gkk~y~i~v~einp~KL----anf-~~~ID~fV~iaC 214 (313)
..+.+|+|+..+.-..+..+++.+++.++++|....+. -+.-++++. ..+ ...+|++|+++.
T Consensus 58 ~~~~Igvi~~~~~~~f~~~l~~gi~~~~~~~gy~~~~~-~~~~~~~~~~~~i~~l~~~~vdGiIi~~~ 124 (346)
T PRK10401 58 VSDTIGVVVMDVSDAFFGALVKAVDLVAQQHQKYVLIG-NSYHEAEKERHAIEVLIRQRCNALIVHSK 124 (346)
T ss_pred CCCEEEEEeCCCCCccHHHHHHHHHHHHHHCCCEEEEE-cCCCChHHHHHHHHHHHhcCCCEEEEeCC
Confidence 45689999998888888889999999999998764332 233344332 222 124999998864
No 179
>cd06319 PBP1_ABC_sugar_binding_like_10 Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems. Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily, which consists of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis.
Probab=34.51 E-value=84 Score=28.01 Aligned_cols=32 Identities=13% Similarity=0.122 Sum_probs=18.6
Q ss_pred EEEEEeCCCCCCcHHHHHHHHHHHHHcCCcEE
Q 042576 156 WGIVLGTLGRQGNPRILERLQKRMEKKGFDYV 187 (313)
Q Consensus 156 ~GIIvgTLg~Q~~~~ii~~l~~ll~~~Gkk~y 187 (313)
+|+|+..+.-..+..+++.+++.+++.|.+..
T Consensus 2 i~vi~~~~~~~~~~~~~~~i~~~~~~~g~~~~ 33 (277)
T cd06319 2 IAYIVSDLRIPFWQIMGRGVKSKAKALGYDAV 33 (277)
T ss_pred eEEEeCCCCchHHHHHHHHHHHHHHhcCCeEE
Confidence 56666555555555566666666666665543
No 180
>PRK15395 methyl-galactoside ABC transporter galactose-binding periplasmic protein MglB; Provisional
Probab=34.24 E-value=1.5e+02 Score=28.05 Aligned_cols=64 Identities=8% Similarity=0.026 Sum_probs=40.6
Q ss_pred cCCEEEEEEeCCCCCCcHHHHHHHHHHHHHcCCcEEEEEeCCCCHHH----HhcCc-CCccEEEEecCC
Q 042576 152 EARTWGIVLGTLGRQGNPRILERLQKRMEKKGFDYVVIMMSEISPAR----VALFE-DSVDAWIQIACP 215 (313)
Q Consensus 152 ~A~~~GIIvgTLg~Q~~~~ii~~l~~ll~~~Gkk~y~i~v~einp~K----Lanf~-~~ID~fV~iaCP 215 (313)
..++||+++..++......+++.+++.+++.|.-..++.-+.-+++. +..+. ..+|++|+.+++
T Consensus 23 ~~~~Igvv~~~~~~~f~~~~~~gi~~~a~~~g~~~~~~~~~~~~~~~~~~~i~~l~~~~vdgiIi~~~~ 91 (330)
T PRK15395 23 ADTRIGVTIYKYDDNFMSVVRKAIEKDAKAAPDVQLLMNDSQNDQSKQNDQIDVLLAKGVKALAINLVD 91 (330)
T ss_pred CCceEEEEEecCcchHHHHHHHHHHHHHHhcCCeEEEEecCCCCHHHHHHHHHHHHHcCCCEEEEeccC
Confidence 56788988887777777788888888888876322222233334332 32332 148888887655
No 181
>cd06274 PBP1_FruR Ligand binding domain of DNA transcription repressor specific for fructose (FruR) and its close homologs. Ligand binding domain of DNA transcription repressor specific for fructose (FruR) and its close homologs, all of which are a member of the LacI-GalR family of bacterial transcription regulators. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to members of the type I periplasmic binding protein superfamily. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor
Probab=34.12 E-value=3.3e+02 Score=24.02 Aligned_cols=130 Identities=11% Similarity=0.094 Sum_probs=61.7
Q ss_pred ccHhHHHHHHHHHHhCCCeEEecCCCCCCCccccCCCCCCCCCCCCCCeEEEecCCcccHH-HHHhhCCCceEEEeCCCC
Q 042576 47 QFASAIRAAKPELEKQGFKVMIPQSKPLSAGEVLGCTAPKIPARESDFNLVFIADGRFHLE-AFMISNPGIKTFRYDPYL 125 (313)
Q Consensus 47 Qf~~~l~~~~~~L~~~g~~v~ipq~~pls~GevLGCt~~~~~~~~~~d~iv~igdGrFHle-~~mi~np~~~~y~yDPys 125 (313)
.|...+..+.+.+++.|+++.+-.... .+......-..... ..+|+++..+... ... --.+..-.+|++.+|-..
T Consensus 13 ~~~~~~~~~~~~~~~~g~~~~~~~~~~-~~~~~~~~i~~l~~--~~vdgiii~~~~~-~~~~~~~~~~~~ipvV~~~~~~ 88 (264)
T cd06274 13 SFARIAKRLEALARERGYQLLIACSDD-DPETERETVETLIA--RQVDALIVAGSLP-PDDPYYLCQKAGLPVVALDRPG 88 (264)
T ss_pred hHHHHHHHHHHHHHHCCCEEEEEeCCC-CHHHHHHHHHHHHH--cCCCEEEEcCCCC-chHHHHHHHhcCCCEEEecCcc
Confidence 445555667777777777765411100 00000000000001 1367777665321 111 111233456777776432
Q ss_pred C--cccccccCh---HHHHHHHHHHHHHHhhcCCEEEEEEeCCCCCCcHHHHHHHHHHHHHcCCc
Q 042576 126 G--KLFLEEYDN---KGMRETRKRAIEKAMKEARTWGIVLGTLGRQGNPRILERLQKRMEKKGFD 185 (313)
Q Consensus 126 ~--~~~~e~~d~---~~~l~~R~~~I~kak~~A~~~GIIvgTLg~Q~~~~ii~~l~~ll~~~Gkk 185 (313)
. .+.....|. .++.... +++ + ..+++|+|.|..+......-.+-.++-++++|.+
T Consensus 89 ~~~~~~~V~~d~~~~g~~~~~~--l~~--~-g~~~i~~i~~~~~~~~~~~R~~gf~~~~~~~~~~ 148 (264)
T cd06274 89 DPSRFPSVVSDNRDGAAELTRE--LLA--A-PPEEVLFLGGLPELSPSRERLAGFRQALADAGLP 148 (264)
T ss_pred CCCCCCEEEEccHHHHHHHHHH--HHH--C-CCCcEEEEeCCCcccchHHHHHHHHHHHHHcCCC
Confidence 1 111112222 2222211 222 5 7789999988766444455567778888888854
No 182
>PF01408 GFO_IDH_MocA: Oxidoreductase family, NAD-binding Rossmann fold; InterPro: IPR000683 This group of enzymes utilise NADP or NAD, and is known as the GFO/IDH/MOCA family in UniProtKB/Swiss-Prot. GFO is a glucose--fructose oxidoreductase, which converts D-glucose and D-fructose into D-gluconolactone and D-glucitol in the sorbitol-gluconate pathway. MOCA is a rhizopine catabolism protein which may catalyse the NADH-dependent dehydrogenase reaction involved in rhizopine catabolism. Other proteins belonging to this family include Gal80, a negative regulator for the expression of lactose and galactose metabolic genes; and several hypothetical proteins from yeast, Escherichia coli and Bacillus subtilis. The oxidoreductase, N-terminal domain is almost always associated with the oxidoreductase, C-terminal domain (see IPR004104 from INTERPRO).; GO: 0016491 oxidoreductase activity; PDB: 1LC0_A 1LC3_A 1GCU_A 3IP3_E 3CEA_C 3EVN_A 3NTQ_A 3NTR_B 3NT5_A 3MZ0_A ....
Probab=33.96 E-value=2.3e+02 Score=22.13 Aligned_cols=89 Identities=22% Similarity=0.193 Sum_probs=54.0
Q ss_pred EEEecCCc---ccHHHHHhhCCCce-EEEeCCCCCcccc-------cc-cChHHHHHH--------------HHHHHHHH
Q 042576 96 LVFIADGR---FHLEAFMISNPGIK-TFRYDPYLGKLFL-------EE-YDNKGMRET--------------RKRAIEKA 149 (313)
Q Consensus 96 iv~igdGr---FHle~~mi~np~~~-~y~yDPys~~~~~-------e~-~d~~~~l~~--------------R~~~I~ka 149 (313)
+.+||-|. .|+..+.-..|... +-.+||...+... .. -|.++|+.. +...+.+|
T Consensus 3 v~iiG~G~~g~~~~~~~~~~~~~~~v~~v~d~~~~~~~~~~~~~~~~~~~~~~~ll~~~~~D~V~I~tp~~~h~~~~~~~ 82 (120)
T PF01408_consen 3 VGIIGAGSIGRRHLRALLRSSPDFEVVAVCDPDPERAEAFAEKYGIPVYTDLEELLADEDVDAVIIATPPSSHAEIAKKA 82 (120)
T ss_dssp EEEESTSHHHHHHHHHHHHTTTTEEEEEEECSSHHHHHHHHHHTTSEEESSHHHHHHHTTESEEEEESSGGGHHHHHHHH
T ss_pred EEEECCcHHHHHHHHHHHhcCCCcEEEEEEeCCHHHHHHHHHHhcccchhHHHHHHHhhcCCEEEEecCCcchHHHHHHH
Confidence 45677765 47767766656655 4578886533221 11 235555552 56666666
Q ss_pred hhcCCEEEEEEeCCCCCCcHHHHHHHHHHHHHcCCcEE
Q 042576 150 MKEARTWGIVLGTLGRQGNPRILERLQKRMEKKGFDYV 187 (313)
Q Consensus 150 k~~A~~~GIIvgTLg~Q~~~~ii~~l~~ll~~~Gkk~y 187 (313)
- ++++ =|+.-+..--+++-+++|.++.+++|+.+.
T Consensus 83 l-~~g~--~v~~EKP~~~~~~~~~~l~~~a~~~~~~~~ 117 (120)
T PF01408_consen 83 L-EAGK--HVLVEKPLALTLEEAEELVEAAKEKGVKVM 117 (120)
T ss_dssp H-HTTS--EEEEESSSSSSHHHHHHHHHHHHHHTSCEE
T ss_pred H-HcCC--EEEEEcCCcCCHHHHHHHHHHHHHhCCEEE
Confidence 6 6665 455566666677777777777777777643
No 183
>PRK10339 DNA-binding transcriptional repressor EbgR; Provisional
Probab=33.66 E-value=76 Score=29.61 Aligned_cols=58 Identities=12% Similarity=0.048 Sum_probs=39.7
Q ss_pred cCCEEEEEEe----CCCCCCcHHHHHHHHHHHHHcCCcEEEEEeCCCCHHHHhcCcCCccEEEEecC
Q 042576 152 EARTWGIVLG----TLGRQGNPRILERLQKRMEKKGFDYVVIMMSEISPARVALFEDSVDAWIQIAC 214 (313)
Q Consensus 152 ~A~~~GIIvg----TLg~Q~~~~ii~~l~~ll~~~Gkk~y~i~v~einp~KLanf~~~ID~fV~iaC 214 (313)
....+|||+. ++.-..+..+++.+++.++++|....+..-. ..+ + ... .+|.+++++.
T Consensus 62 ~~~~i~v~~~~~~~~~~~~f~~~l~~~i~~~~~~~g~~~~~~~~~--~~~-~-~~~-~vDgiI~~~~ 123 (327)
T PRK10339 62 QHHILAIYSYQQELEINDPYYLAIRHGIETQCEKLGIELTNCYEH--SGL-P-DIK-NVTGILIVGK 123 (327)
T ss_pred cccEEEEEEccccccccCchHHHHHHHHHHHHHHCCCEEEEeecc--ccc-c-ccc-cCCEEEEeCC
Confidence 4567888884 5666677789999999999999775443221 121 1 234 5999998774
No 184
>PF01729 QRPTase_C: Quinolinate phosphoribosyl transferase, C-terminal domain; InterPro: IPR002638 Quinolinate phosphoribosyl transferase (QPRTase) or nicotinate-nucleotide pyrophosphorylase 2.4.2.19 from EC is involved in the de novo synthesis of NAD in both prokaryotes and eukaryotes. It catalyses the reaction of quinolinic acid with 5-phosphoribosyl-1-pyrophosphate (PRPP) in the presence of Mg2+ to give rise to nicotinic acid mononucleotide (NaMN), pyrophosphate and carbon dioxide [, ]. Unlike IPR004393 from INTERPRO, this domain also includes the molybdenum transport system protein ModD.; GO: 0004514 nicotinate-nucleotide diphosphorylase (carboxylating) activity, 0009435 NAD biosynthetic process; PDB: 3C2O_A 3C2F_A 3C2E_A 3C2R_A 3C2V_A 1QPN_E 1QPO_A 1QPQ_F 1QPR_E 2I14_D ....
Probab=33.54 E-value=78 Score=27.97 Aligned_cols=82 Identities=18% Similarity=0.141 Sum_probs=55.4
Q ss_pred EEeCCCCCcccccccChHHHHHHHHHHHHHHhhcCCEEEEEEeCCCCCCcHHHHHHHHHHHHHcCCcEEEEEeCCCCHHH
Q 042576 119 FRYDPYLGKLFLEEYDNKGMRETRKRAIEKAMKEARTWGIVLGTLGRQGNPRILERLQKRMEKKGFDYVVIMMSEISPAR 198 (313)
Q Consensus 119 y~yDPys~~~~~e~~d~~~~l~~R~~~I~kak~~A~~~GIIvgTLg~Q~~~~ii~~l~~ll~~~Gkk~y~i~v~einp~K 198 (313)
-+..|...++..|-.+.+ ..+.|. +++.-+|.+=+. +++-++++.+.|++.+.+..+.+.|.||++.
T Consensus 74 ~~~~~~~~~I~VEv~~~e--------e~~ea~-~~g~d~I~lD~~----~~~~~~~~v~~l~~~~~~v~ie~SGGI~~~n 140 (169)
T PF01729_consen 74 RQAAPEKKKIEVEVENLE--------EAEEAL-EAGADIIMLDNM----SPEDLKEAVEELRELNPRVKIEASGGITLEN 140 (169)
T ss_dssp HHHSTTTSEEEEEESSHH--------HHHHHH-HTT-SEEEEES-----CHHHHHHHHHHHHHHTTTSEEEEESSSSTTT
T ss_pred HHhCCCCceEEEEcCCHH--------HHHHHH-HhCCCEEEecCc----CHHHHHHHHHHHhhcCCcEEEEEECCCCHHH
Confidence 344555554554544432 334555 666667777776 6788888888888888889999999999999
Q ss_pred HhcCcC-CccEEEEec
Q 042576 199 VALFED-SVDAWIQIA 213 (313)
Q Consensus 199 Lanf~~-~ID~fV~ia 213 (313)
+..|.. .||.++.-+
T Consensus 141 i~~ya~~gvD~isvg~ 156 (169)
T PF01729_consen 141 IAEYAKTGVDVISVGS 156 (169)
T ss_dssp HHHHHHTT-SEEEECH
T ss_pred HHHHHhcCCCEEEcCh
Confidence 998851 478876543
No 185
>cd01391 Periplasmic_Binding_Protein_Type_1 Type 1 periplasmic binding fold superfamily. Type 1 periplasmic binding fold superfamily. This model and hierarchy represent the ligand binding domains of the LacI family of transcriptional regulators, periplasmic binding proteins of the ABC-type transport systems, the family C G-protein couples receptors (GPCRs), membrane bound guanylyl cyclases including the family of natriuretic peptide receptors (NPRs), and the N-terminal leucine/isoleucine/valine- binding protein (LIVBP)-like domains of the ionotropic glutamate receptors (iGluRs). In LacI-like transcriptional regulator and the bacterial periplasmic binding proteins the ligands are monosaccharides including lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars, with a few exceptions. Periplasmic sugar binding proteins are one of the components of ABC transporters and are involved in the active transport of water-soluble ligands. The LacI family of proteins con
Probab=33.49 E-value=3e+02 Score=23.29 Aligned_cols=39 Identities=21% Similarity=0.299 Sum_probs=27.9
Q ss_pred cCCEEEEEEeCCCCCCcHHHHHHHHHHHHHcCCcEEEEEe
Q 042576 152 EARTWGIVLGTLGRQGNPRILERLQKRMEKKGFDYVVIMM 191 (313)
Q Consensus 152 ~A~~~GIIvgTLg~Q~~~~ii~~l~~ll~~~Gkk~y~i~v 191 (313)
..+++|+|.+... .......+.+++.++++|.+...+..
T Consensus 123 ~~~~i~~i~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~ 161 (269)
T cd01391 123 GWKRVALIYGDDG-AYGRERLEGFKAALKKAGIEVVAIEY 161 (269)
T ss_pred CCceEEEEecCCc-chhhHHHHHHHHHHHhcCcEEEeccc
Confidence 4678999988775 55566778888889888865544433
No 186
>PRK09701 D-allose transporter subunit; Provisional
Probab=33.33 E-value=1.3e+02 Score=28.18 Aligned_cols=62 Identities=13% Similarity=0.067 Sum_probs=36.3
Q ss_pred cCCEEEEEEeCCCCCCcHHHHHHHHHHHHHcCCcEEEEE-eCCCCHHH----HhcCc-CCccEEEEec
Q 042576 152 EARTWGIVLGTLGRQGNPRILERLQKRMEKKGFDYVVIM-MSEISPAR----VALFE-DSVDAWIQIA 213 (313)
Q Consensus 152 ~A~~~GIIvgTLg~Q~~~~ii~~l~~ll~~~Gkk~y~i~-v~einp~K----Lanf~-~~ID~fV~ia 213 (313)
-+..+|+|+.++.-.....+++.+++.+++.|....++. -++-++++ |.++- ..+|++|+.+
T Consensus 23 ~~~~Igvi~~~~~~~f~~~~~~gi~~~a~~~g~~v~~~~~~~~~~~~~~~~~i~~l~~~~vDgiIi~~ 90 (311)
T PRK09701 23 AAAEYAVVLKTLSNPFWVDMKKGIEDEAKTLGVSVDIFASPSEGDFQSQLQLFEDLSNKNYKGIAFAP 90 (311)
T ss_pred cCCeEEEEeCCCCCHHHHHHHHHHHHHHHHcCCeEEEecCCCCCCHHHHHHHHHHHHHcCCCEEEEeC
Confidence 456778877776655666777777777777776655442 12223322 33331 1377776653
No 187
>cd01545 PBP1_SalR Ligand-binding domain of DNA transcription repressor SalR, a member of the LacI-GalR family of bacterial transcription regulators. Ligand-binding domain of DNA transcription repressor SalR, a member of the LacI-GalR family of bacterial transcription regulators. The SalR binds to glucose based compound Salicin which is chemically related to aspirin. The ligand-binding of SalR is structurally homologous to the periplasmic sugar-binding domain of ABC-transporters and both domains contain the type I periplasmic binding protein-like fold. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the type I periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand bind
Probab=33.16 E-value=3.4e+02 Score=23.86 Aligned_cols=35 Identities=14% Similarity=0.290 Sum_probs=23.1
Q ss_pred cCCEEEEEEeCCCCCCcHHHHHHHHHHHHHcCCcE
Q 042576 152 EARTWGIVLGTLGRQGNPRILERLQKRMEKKGFDY 186 (313)
Q Consensus 152 ~A~~~GIIvgTLg~Q~~~~ii~~l~~ll~~~Gkk~ 186 (313)
..+++++|-|..+-.....-.+-.++.++++|.+.
T Consensus 117 g~~~i~~i~~~~~~~~~~~R~~Gf~~~~~~~~~~~ 151 (270)
T cd01545 117 GHRRIAFIAGPPDHRASAERLEGYRDALAEAGLPL 151 (270)
T ss_pred CCceEEEEeCCCCchhHHHHHHHHHHHHHHcCCCC
Confidence 56789988877654333344555677777777664
No 188
>TIGR01754 flav_RNR ribonucleotide reductase-associated flavodoxin, putative. This model represents a family of proteins found immediately downstream of ribonucleotide reductase genes in Xyella fastidiosa and some Gram-positive bacteria. It appears to be a highly divergent flavodoxin of the short chain type, more like the flavodoxins of the sulfate-reducing genus Desulfovibrio than like the NifF flavodoxins associated with nitrogen fixation.
Probab=33.01 E-value=82 Score=26.17 Aligned_cols=57 Identities=12% Similarity=0.075 Sum_probs=35.1
Q ss_pred EEEEEEeCCCCCCcHHHHHHHHHHHHHcCCcEE-EEEeCCCCHHHHhcCcCCccEEEEecCC
Q 042576 155 TWGIVLGTLGRQGNPRILERLQKRMEKKGFDYV-VIMMSEISPARVALFEDSVDAWIQIACP 215 (313)
Q Consensus 155 ~~GIIvgTLg~Q~~~~ii~~l~~ll~~~Gkk~y-~i~v~einp~KLanf~~~ID~fV~iaCP 215 (313)
++.||.+|..| +...++++|.+.|+..|.++- +.-+.+++.. ..++. +.|+ |+++||
T Consensus 2 ~i~IiY~S~tG-nTe~iA~~ia~~l~~~g~~v~~~~~~~~~~~~-~~~~~-~~d~-iilgs~ 59 (140)
T TIGR01754 2 RILLAYLSLSG-NTEEVAFMIQDYLQKDGHEVDILHRIGTLADA-PLDPE-NYDL-VFLGTW 59 (140)
T ss_pred eEEEEEECCCC-hHHHHHHHHHHHHhhCCeeEEecccccccccC-cCChh-hCCE-EEEEcC
Confidence 46899999653 356789999999998887754 2333433221 12333 4566 455555
No 189
>TIGR01205 D_ala_D_alaTIGR D-alanine--D-alanine ligase. but a number of antibiotic resistance proteins score above the trusted cutoff of this model.
Probab=32.87 E-value=1.6e+02 Score=27.60 Aligned_cols=58 Identities=12% Similarity=0.251 Sum_probs=43.7
Q ss_pred EEEEEEeCCCCCC--cHHHHHHHHHHHHHcCCcEEEEEeCCCC-------HHHHhcC----cCCccEEEEec
Q 042576 155 TWGIVLGTLGRQG--NPRILERLQKRMEKKGFDYVVIMMSEIS-------PARVALF----EDSVDAWIQIA 213 (313)
Q Consensus 155 ~~GIIvgTLg~Q~--~~~ii~~l~~ll~~~Gkk~y~i~v~ein-------p~KLanf----~~~ID~fV~ia 213 (313)
++|||.|-.+-.. ++.-..++.+-|++.|.+++++-+.+.+ .+.+..+ . ++|+.+.+.
T Consensus 1 ~~~~~~gg~s~e~~~s~~s~~~i~~al~~~g~~v~~i~~~~~~~~~~~~~~~~~~~~~~~~~-~~D~v~~~~ 71 (315)
T TIGR01205 1 RVAVLFGGKSAEHEISLVSAAAVLKALRDLGYDVYPVDIDKMGSWTYKDLPQLILELGALLE-GIDVVFPVL 71 (315)
T ss_pred CEEEEeCCCCCCeeeeHHHHHHHHHHHhhcCCEEEEEeecCCccccccchHHHHhhccccCC-CCCEEEEec
Confidence 4899999998877 4788889999999999999999888743 2223321 3 588888753
No 190
>COG0279 GmhA Phosphoheptose isomerase [Carbohydrate transport and metabolism]
Probab=32.73 E-value=2.3e+02 Score=25.55 Aligned_cols=103 Identities=18% Similarity=0.202 Sum_probs=65.6
Q ss_pred CCeEEEec--CCcccHHHHHhhCCCceEEEeCCCCCccccc--ccChHHHHHHHHHHHHHHhhcCCEEEEEEeCCCCCCc
Q 042576 93 DFNLVFIA--DGRFHLEAFMISNPGIKTFRYDPYLGKLFLE--EYDNKGMRETRKRAIEKAMKEARTWGIVLGTLGRQGN 168 (313)
Q Consensus 93 ~d~iv~ig--dGrFHle~~mi~np~~~~y~yDPys~~~~~e--~~d~~~~l~~R~~~I~kak~~A~~~GIIvgTLg~Q~~ 168 (313)
.|+..|.+ -|||+.+ -|..|+....-.+..+|.. +|..+.+..|-..+ .- ...=+-|=++|.| ++
T Consensus 54 adAqHfaael~gRf~~e-----R~~lpaIaLt~dsS~lTai~NDy~yd~vFsRqveA---~g-~~GDvLigISTSG--NS 122 (176)
T COG0279 54 ADAQHFAAELTGRFEKE-----RPSLPAIALSTDSSVLTAIANDYGYDEVFSRQVEA---LG-QPGDVLIGISTSG--NS 122 (176)
T ss_pred hhHHHHHHHHhhHHHhc-----CCCCCeeEeecccHHHhhhhccccHHHHHHHHHHh---cC-CCCCEEEEEeCCC--CC
Confidence 45555555 3676653 4677777666555555543 45566665544333 33 3344557778887 88
Q ss_pred HHHHHHHHHHHHHcCCcEEEEEeCCCCHHHHhcCcCCccEEE
Q 042576 169 PRILERLQKRMEKKGFDYVVIMMSEISPARVALFEDSVDAWI 210 (313)
Q Consensus 169 ~~ii~~l~~ll~~~Gkk~y~i~v~einp~KLanf~~~ID~fV 210 (313)
+.+++.++.- +.|...+|.|.-=+=.|++.|- |++..|
T Consensus 123 ~nVl~Ai~~A---k~~gm~vI~ltG~~GG~~~~~~-D~~i~V 160 (176)
T COG0279 123 KNVLKAIEAA---KEKGMTVIALTGKDGGKLAGLL-DVEIRV 160 (176)
T ss_pred HHHHHHHHHH---HHcCCEEEEEecCCCccccccc-ceEEec
Confidence 8888877743 4456778888888999999998 555443
No 191
>TIGR00114 lumazine-synth 6,7-dimethyl-8-ribityllumazine synthase. Archaeal members of this family are considered putative, although included in the seed and scoring above the trusted cutoff.
Probab=32.49 E-value=1.4e+02 Score=25.71 Aligned_cols=85 Identities=25% Similarity=0.300 Sum_probs=52.2
Q ss_pred EEEEEEeCCCCCCcHHHHHHHHHHHHHcCCcE---EEEEeCCCC-----HHHHhcCcCCccEEEEecCC-Cccc------
Q 042576 155 TWGIVLGTLGRQGNPRILERLQKRMEKKGFDY---VVIMMSEIS-----PARVALFEDSVDAWIQIACP-RLSI------ 219 (313)
Q Consensus 155 ~~GIIvgTLg~Q~~~~ii~~l~~ll~~~Gkk~---y~i~v~ein-----p~KLanf~~~ID~fV~iaCP-rlsi------ 219 (313)
+||||++..-..-.-.+++-..+.|+++|... .++.|--.+ ..+|+.=. .+|++|-++|- |...
T Consensus 2 ri~IV~s~~n~~i~~~L~~ga~~~l~~~g~~~~~i~v~~VPGa~EiP~a~~~l~~~~-~~DavI~LG~VIrG~T~H~e~v 80 (138)
T TIGR00114 2 RVGIVIARFNRDITDMLLKGAIDALKRLGAEVDNIDVIWVPGAFELPLAVKKLAETG-KYDAVIALGCVIRGGTPHFEYV 80 (138)
T ss_pred EEEEEEecCCHHHHHHHHHHHHHHHHHcCCCccceEEEECCcHHHHHHHHHHHHhcC-CCCEEEEEeeEEeCCCchhHHH
Confidence 58899986554444445555566788888653 355444322 13555445 69999999996 1111
Q ss_pred ---------cccCCCCCc----ccCHHHHHHHhC
Q 042576 220 ---------DWGDAFTKP----LLTPFEAEIALG 240 (313)
Q Consensus 220 ---------d~~~~f~kP----vLTPyE~~vAL~ 240 (313)
+=+-++.+| ||||.-.+-|+.
T Consensus 81 ~~~v~~gl~~~sl~~~~PV~~GvLt~~~~eQa~~ 114 (138)
T TIGR00114 81 ADEAAKGIADLALDYDKPVIFGILTTGTIEQAIE 114 (138)
T ss_pred HHHHHHHHHHHHhhhCCCEEEEecCCCCHHHHHH
Confidence 123357788 477777766664
No 192
>PRK09426 methylmalonyl-CoA mutase; Reviewed
Probab=32.47 E-value=1e+02 Score=33.55 Aligned_cols=72 Identities=17% Similarity=0.289 Sum_probs=46.9
Q ss_pred HHHHHhh-cCCEEEEEEeCCCCCCcHHHHHHHHHHHHHcCCcEEEEEeC-CCCHHHHhcCc-CCccEEEEecCCCccc
Q 042576 145 AIEKAMK-EARTWGIVLGTLGRQGNPRILERLQKRMEKKGFDYVVIMMS-EISPARVALFE-DSVDAWIQIACPRLSI 219 (313)
Q Consensus 145 ~I~kak~-~A~~~GIIvgTLg~Q~~~~ii~~l~~ll~~~Gkk~y~i~v~-einp~KLanf~-~~ID~fV~iaCPrlsi 219 (313)
.++.|++ ++..++ ++++- ..+.+.+..+.+.|+++|.+-.+++++ .+-|+..+.+. ..+|.|+-..|+-..+
T Consensus 625 ~v~aa~~~~a~ivv--lcs~d-~~~~e~~~~l~~~Lk~~G~~~v~vl~GG~~~~~~~~~l~~aGvD~~i~~g~d~~~~ 699 (714)
T PRK09426 625 AARQAVENDVHVVG--VSSLA-AGHKTLVPALIEALKKLGREDIMVVVGGVIPPQDYDFLYEAGVAAIFGPGTVIADA 699 (714)
T ss_pred HHHHHHHcCCCEEE--Eeccc-hhhHHHHHHHHHHHHhcCCCCcEEEEeCCCChhhHHHHHhCCCCEEECCCCCHHHH
Confidence 5556651 344443 34442 678889999999999999875545555 54554333232 1499999999987654
No 193
>PF09547 Spore_IV_A: Stage IV sporulation protein A (spore_IV_A); InterPro: IPR014201 This entry is designated stage IV sporulation protein A. It acts in the mother cell compartment and plays a role in spore coat morphogenesis []. A comparative genome analysis of all sequenced genomes of Firmicutes shows that the proteins are strictly conserved among the sub-set of endospore-forming species.
Probab=32.46 E-value=72 Score=32.91 Aligned_cols=71 Identities=24% Similarity=0.396 Sum_probs=48.9
Q ss_pred cCCEEEEEEeC------CCCCCcHHHHHHHHHHHHHcCCcEEEEEeCCCCH-----HHHh-cCcCCccE-EEEecCCCcc
Q 042576 152 EARTWGIVLGT------LGRQGNPRILERLQKRMEKKGFDYVVIMMSEISP-----ARVA-LFEDSVDA-WIQIACPRLS 218 (313)
Q Consensus 152 ~A~~~GIIvgT------Lg~Q~~~~ii~~l~~ll~~~Gkk~y~i~v~einp-----~KLa-nf~~~ID~-fV~iaCPrls 218 (313)
+-.++||||.| +.|.+|.+.=++.-+.|++-||.+.+++=+ ..| .+|+ .+....|+ .+-+.|-++.
T Consensus 143 dHSTIGiVVTTDGSi~dipRe~Y~eAEervI~ELk~igKPFvillNs-~~P~s~et~~L~~eL~ekY~vpVlpvnc~~l~ 221 (492)
T PF09547_consen 143 DHSTIGIVVTTDGSITDIPRENYVEAEERVIEELKEIGKPFVILLNS-TKPYSEETQELAEELEEKYDVPVLPVNCEQLR 221 (492)
T ss_pred cCCceeEEEecCCCccCCChHHHHHHHHHHHHHHHHhCCCEEEEEeC-CCCCCHHHHHHHHHHHHHhCCcEEEeehHHcC
Confidence 66799999977 568899999999999999999987666544 332 1222 11112444 3567898887
Q ss_pred ccccC
Q 042576 219 IDWGD 223 (313)
Q Consensus 219 id~~~ 223 (313)
-+|-.
T Consensus 222 ~~DI~ 226 (492)
T PF09547_consen 222 EEDIT 226 (492)
T ss_pred HHHHH
Confidence 76644
No 194
>TIGR03018 pepcterm_TyrKin exopolysaccharide/PEPCTERM locus tyrosine autokinase. Members of this protein family are related to a known protein-tyrosine autokinase and to numerous homologs from exopolysaccharide biosynthesis region proteins, many of which are designated as chain length determinants. Most members of this family contain a short region, immediately C-terminal to the region modeled here, with an abundance of Tyr residues. These C-terminal tyrosine residues are likely to be autophosphorylation sites. Some members of this family are fusion proteins.
Probab=32.10 E-value=2e+02 Score=25.38 Aligned_cols=61 Identities=13% Similarity=0.126 Sum_probs=43.1
Q ss_pred hHHHHHHHHHHHHHH----hhcCCEEEEEEeCCCCCCcHHHHHHHHHHHHH-cCCcEEEEEeCCCC
Q 042576 135 NKGMRETRKRAIEKA----MKEARTWGIVLGTLGRQGNPRILERLQKRMEK-KGFDYVVIMMSEIS 195 (313)
Q Consensus 135 ~~~~l~~R~~~I~ka----k~~A~~~GIIvgTLg~Q~~~~ii~~l~~ll~~-~Gkk~y~i~v~ein 195 (313)
.+.+.+.|..++..+ .....++=.|+|.+|+.|.-.+.-.|-..+.+ .|+++.+|=++--+
T Consensus 12 ~~~~~~l~~~l~~~~~~~~~~~~~~vi~v~s~kgG~GkSt~a~nLA~~la~~~g~~VLlvD~D~~~ 77 (207)
T TIGR03018 12 AEEFRKIKRPLLANAFSANRKKNNNLIMVTSSLPGEGKSFTAINLAISLAQEYDKTVLLIDADLRR 77 (207)
T ss_pred HHHHHHHHHHHHHhccccccCCCCeEEEEECCCCCCCHHHHHHHHHHHHHHhcCCeEEEEECCCCC
Confidence 345667777777655 21234455777999999999999999998875 69887666555443
No 195
>cd01571 NAPRTase_B Nicotinate phosphoribosyltransferase (NAPRTase), subgroup B. Nicotinate phosphoribosyltransferase catalyses the formation of NAMN and PPi from 5-phosphoribosy -1-pyrophosphate (PRPP) and nicotinic acid, this is the first, and also rate limiting, reaction in the NAD salvage synthesis. This salvage pathway serves to recycle NAD degradation products.
Probab=31.99 E-value=66 Score=31.00 Aligned_cols=56 Identities=16% Similarity=0.252 Sum_probs=42.4
Q ss_pred CEEEEEEeCCCC--CCcHHHHHHHHHHHHHcC-CcEEEEEeCCCCHHHHhcCcC-CccEE
Q 042576 154 RTWGIVLGTLGR--QGNPRILERLQKRMEKKG-FDYVVIMMSEISPARVALFED-SVDAW 209 (313)
Q Consensus 154 ~~~GIIvgTLg~--Q~~~~ii~~l~~ll~~~G-kk~y~i~v~einp~KLanf~~-~ID~f 209 (313)
+..+|.+=+.++ -..++.++++++.++..| .+..+.+.|.||+++++.|.. .||++
T Consensus 211 ~~d~I~lDn~~~~~G~~~~~~~~~~~~l~~~g~~~~~ieaSGgI~~~~i~~~a~~gvD~i 270 (302)
T cd01571 211 KLDGVRLDTPSSRRGVFRYLIREVRWALDIRGYKHVKIFVSGGLDEEDIKELEDVGVDAF 270 (302)
T ss_pred CCcEEEECCCCCCCCCHHHHHHHHHHHHHhCCCCCeEEEEeCCCCHHHHHHHHHcCCCEE
Confidence 346777777531 126677899999999887 667788889999999999852 38876
No 196
>cd06267 PBP1_LacI_sugar_binding_like Ligand binding domain of the LacI tanscriptional regulator family belonging to the type I periplasmic-binding fold protein superfamily. Ligand binding domain of the LacI tanscriptional regulator family belonging to the type I periplasmic-binding fold protein superfamily. In most cases, ligands are monosaccharide including lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars. The LacI family of proteins consists of transcriptional regulators related to the lac repressor. In this case, the domain sugar binding changes the DNA binding activity of the repressor domain.
Probab=31.93 E-value=90 Score=27.10 Aligned_cols=25 Identities=16% Similarity=0.207 Sum_probs=13.2
Q ss_pred HHHHHHHHHHHcCCcEEEEEeCCCCH
Q 042576 171 ILERLQKRMEKKGFDYVVIMMSEISP 196 (313)
Q Consensus 171 ii~~l~~ll~~~Gkk~y~i~v~einp 196 (313)
.++.+++ +.+.+...+++.....+.
T Consensus 44 ~~~~~~~-~~~~~~d~iii~~~~~~~ 68 (264)
T cd06267 44 EREALEL-LLSRRVDGIILAPSRLDD 68 (264)
T ss_pred HHHHHHH-HHHcCcCEEEEecCCcch
Confidence 3444444 445566666665555443
No 197
>PRK02910 light-independent protochlorophyllide reductase subunit B; Provisional
Probab=31.77 E-value=1.1e+02 Score=31.60 Aligned_cols=76 Identities=17% Similarity=0.222 Sum_probs=54.8
Q ss_pred CCEEEEEEeCCCCCCcHHHHHHHHHHHHHcCCcEEEEEeCCCCHHHHhcCcCCccEEEEec-CCCccccc----cCCCCC
Q 042576 153 ARTWGIVLGTLGRQGNPRILERLQKRMEKKGFDYVVIMMSEISPARVALFEDSVDAWIQIA-CPRLSIDW----GDAFTK 227 (313)
Q Consensus 153 A~~~GIIvgTLg~Q~~~~ii~~l~~ll~~~Gkk~y~i~v~einp~KLanf~~~ID~fV~ia-CPrlsid~----~~~f~k 227 (313)
.+++-||=.+..+-..+.=++.|+++|+..|.+.-.+.-+.-+.+.|.+.+ ++++++. ||+..... .+.|-.
T Consensus 158 ~~~VNIiG~~~l~f~~~~D~~EikrlL~~~Gi~vn~v~p~g~s~~di~~l~---~A~~nivl~~~~g~~~A~~Lee~fGi 234 (519)
T PRK02910 158 RPSVNLLGPTALGFHHRDDLTELRRLLATLGIDVNVVAPLGASPADLKRLP---AAWFNVVLYREIGESAARYLEREFGQ 234 (519)
T ss_pred CCeEEEEecCccCCCChhHHHHHHHHHHHcCCeEEEEeCCCCCHHHHHhcc---cCcEEEEeCHHHHHHHHHHHHHHhCC
Confidence 346766655544444566667799999999999999888899999999998 4555554 99855432 356788
Q ss_pred cccC
Q 042576 228 PLLT 231 (313)
Q Consensus 228 PvLT 231 (313)
|.+.
T Consensus 235 P~i~ 238 (519)
T PRK02910 235 PYVK 238 (519)
T ss_pred cccc
Confidence 8764
No 198
>TIGR02955 TMAO_TorT TMAO reductase system periplasmic protein TorT. Members of this family are the periplasmic protein TorT which, together with the the TorS/TorR histidine kinase/response regulator system, regulates expression of the torCAD operon for trimethylamine N-oxide reductase (TMAO reductase). It appears to bind an inducer for TMAO reductase, and shows homology to a periplasmic D-ribose binding protein.
Probab=31.61 E-value=1.1e+02 Score=28.11 Aligned_cols=36 Identities=11% Similarity=0.008 Sum_probs=21.9
Q ss_pred EEEEEeCCCCCCcHHHHHHHHHHHHHcCCcEEEEEe
Q 042576 156 WGIVLGTLGRQGNPRILERLQKRMEKKGFDYVVIMM 191 (313)
Q Consensus 156 ~GIIvgTLg~Q~~~~ii~~l~~ll~~~Gkk~y~i~v 191 (313)
+|+|+.++.-.....+++-+++.++++|....+...
T Consensus 2 igvvvp~~~n~f~~~~~~gi~~~a~~~g~~v~~~~~ 37 (295)
T TIGR02955 2 LCALYPHLKDSYWLSINYGMVEQAKHLGVELKVLEA 37 (295)
T ss_pred eeEEecCCCcHHHHHHHHHHHHHHHHhCCEEEEEcC
Confidence 566666665555556666666666666655554433
No 199
>PRK05319 rplD 50S ribosomal protein L4; Provisional
Probab=31.61 E-value=3.5e+02 Score=24.61 Aligned_cols=115 Identities=23% Similarity=0.240 Sum_probs=62.2
Q ss_pred CCCCCccccCCCCCCCC--C--C---CCCCeEEEecCCcccHHHHHhhCCCceEEEeCCCCCcccccccChHHHHHHHHH
Q 042576 72 KPLSAGEVLGCTAPKIP--A--R---ESDFNLVFIADGRFHLEAFMISNPGIKTFRYDPYLGKLFLEEYDNKGMRETRKR 144 (313)
Q Consensus 72 ~pls~GevLGCt~~~~~--~--~---~~~d~iv~igdGrFHle~~mi~np~~~~y~yDPys~~~~~e~~d~~~~l~~R~~ 144 (313)
+....+||-|.+.-.-+ . . ....+=+|.|+|..|. | +|- . |+.++-. ..+-+..|..
T Consensus 49 ~tk~r~ev~GsgrK~~~QKGTGrAR~Gs~rsP~~rGGg~afg-------p-kpr-~---~~~klnk----K~~~lAl~~a 112 (205)
T PRK05319 49 ATKTRSEVSGGGKKPWRQKGTGRARQGSIRSPQWRGGGVVFG-------P-KPR-D---YSQKLNK----KVRRLALRSA 112 (205)
T ss_pred cCCcccccCCCCCCCCCCCCCCccCcCcccCCcccCCeeeCC-------C-Ccc-c---hhhhcCH----HHHHHHHHHH
Confidence 44556778776431110 0 0 0123457899998873 3 332 2 2233321 3445667777
Q ss_pred HHHHHhhcCCEEEEEEeCCCCCCcHHHHHHHHHHHHHcCCcEEEEEeCCCCHH-HHh--cCcCCccE
Q 042576 145 AIEKAMKEARTWGIVLGTLGRQGNPRILERLQKRMEKKGFDYVVIMMSEISPA-RVA--LFEDSVDA 208 (313)
Q Consensus 145 ~I~kak~~A~~~GIIvgTLg~Q~~~~ii~~l~~ll~~~Gkk~y~i~v~einp~-KLa--nf~~~ID~ 208 (313)
+-.+++ ..+. +||..+.... + =.+.+.++|++.|.+..+|++++.+.. .++ |++ .+|+
T Consensus 113 Ls~k~~-~~~l--~Vvd~~~~~~-~-KTk~~~~~l~~lg~~~~Lii~~~~~~n~~~a~rNi~-~v~v 173 (205)
T PRK05319 113 LSEKAR-EGRL--VVVDDLSLEA-P-KTKELAAKLKNLGLKKVLIVTDEVDENLYLSARNLP-NVDV 173 (205)
T ss_pred HHHHHh-cCCe--EEEeccccCC-C-CHHHHHHHHHHcCCCceEEEECCCchHHHHHHhCCC-CcEE
Confidence 777777 5554 4666654222 1 134566777777866677777765543 222 666 5665
No 200
>TIGR03449 mycothiol_MshA UDP-N-acetylglucosamine: 1L-myo-inositol-1-phosphate 1-alpha-D-N-acetylglucosaminyltransferase. Members of this protein family, found exclusively in the Actinobacteria, are MshA, the glycosyltransferase of mycothiol biosynthesis. Mycothiol replaces glutathione in these species.
Probab=31.58 E-value=1.5e+02 Score=28.32 Aligned_cols=59 Identities=15% Similarity=0.105 Sum_probs=37.1
Q ss_pred EEEEEEeCCCCCCcHHHHHHHHHHHHHcCCcEEEEEeCCCCHHHHhcCcCCccEEEEecC
Q 042576 155 TWGIVLGTLGRQGNPRILERLQKRMEKKGFDYVVIMMSEISPARVALFEDSVDAWIQIAC 214 (313)
Q Consensus 155 ~~GIIvgTLg~Q~~~~ii~~l~~ll~~~Gkk~y~i~v~einp~KLanf~~~ID~fV~iaC 214 (313)
.--+|+|.-...| ..-.+.+++++++.|....+.++|.++.+.+..+-...|+||+.+-
T Consensus 253 ~~l~ivG~~~~~g-~~~~~~l~~~~~~~~l~~~v~~~g~~~~~~~~~~l~~ad~~v~ps~ 311 (405)
T TIGR03449 253 LRVIVVGGPSGSG-LATPDALIELAAELGIADRVRFLPPRPPEELVHVYRAADVVAVPSY 311 (405)
T ss_pred eEEEEEeCCCCCc-chHHHHHHHHHHHcCCCceEEECCCCCHHHHHHHHHhCCEEEECCC
Confidence 4456676422223 1223567777777777667778888877776654326899987654
No 201
>PRK11914 diacylglycerol kinase; Reviewed
Probab=31.56 E-value=1.8e+02 Score=27.50 Aligned_cols=39 Identities=26% Similarity=0.411 Sum_probs=23.8
Q ss_pred CEEEEEEeCCCCCCc-HHHHHHHHHHHHHcCCcEEEEEeC
Q 042576 154 RTWGIVLGTLGRQGN-PRILERLQKRMEKKGFDYVVIMMS 192 (313)
Q Consensus 154 ~~~GIIvgTLg~Q~~-~~ii~~l~~ll~~~Gkk~y~i~v~ 192 (313)
+++.||++..++.|. .+..+++++.|+++|.++.++...
T Consensus 9 ~~~~iI~NP~sG~g~~~~~~~~~~~~l~~~g~~~~~~~t~ 48 (306)
T PRK11914 9 GKVTVLTNPLSGHGAAPHAAERAIARLHHRGVDVVEIVGT 48 (306)
T ss_pred ceEEEEECCCCCCCcHHHHHHHHHHHHHHcCCeEEEEEeC
Confidence 456677777766554 456666666677667665444443
No 202
>PLN02949 transferase, transferring glycosyl groups
Probab=31.09 E-value=80 Score=32.12 Aligned_cols=72 Identities=17% Similarity=0.130 Sum_probs=49.7
Q ss_pred EEEEEeCCCCCCcHHHHHHHHHHHHHcCCcEEEEEeCCCCHHHHhc-CcCCccEEEEecCCCccccccCCCCCcccCHHH
Q 042576 156 WGIVLGTLGRQGNPRILERLQKRMEKKGFDYVVIMMSEISPARVAL-FEDSVDAWIQIACPRLSIDWGDAFTKPLLTPFE 234 (313)
Q Consensus 156 ~GIIvgTLg~Q~~~~ii~~l~~ll~~~Gkk~y~i~v~einp~KLan-f~~~ID~fV~iaCPrlsid~~~~f~kPvLTPyE 234 (313)
--+|+|.-..+++.+..+.|++++++.|..-.+.+++.++-+.+.. +. ..|++|..+..+ .|.- ++-|
T Consensus 305 ~LvIvG~~~~~~~~~~~~eL~~la~~l~L~~~V~f~g~v~~~el~~ll~-~a~~~v~~s~~E-------~FGi---vvlE 373 (463)
T PLN02949 305 KLQFVGSCRNKEDEERLQKLKDRAKELGLDGDVEFHKNVSYRDLVRLLG-GAVAGLHSMIDE-------HFGI---SVVE 373 (463)
T ss_pred EEEEEeCCCCcccHHHHHHHHHHHHHcCCCCcEEEeCCCCHHHHHHHHH-hCcEEEeCCccC-------CCCh---HHHH
Confidence 3467776544556677789999999998877777789888666664 45 688998765433 3543 4667
Q ss_pred HHHH
Q 042576 235 AEIA 238 (313)
Q Consensus 235 ~~vA 238 (313)
+..+
T Consensus 374 AMA~ 377 (463)
T PLN02949 374 YMAA 377 (463)
T ss_pred HHHc
Confidence 7653
No 203
>cd06323 PBP1_ribose_binding Periplasmic sugar-binding domain of the thermophilic Thermoanaerobacter tengcongensis ribose binding protein (ttRBP) and its mesophilic homologs. Periplasmic sugar-binding domain of the thermophilic Thermoanaerobacter tengcongensis ribose binding protein (ttRBP) and its mesophilic homologs. Members of this group are belonging to the type I periplasmic binding protein superfamily, whose members are involved in chemotaxis, ATP-binding cassette transport, and intercellular communication in central nervous system. The thermophilic and mesophilic ribose-binding proteins are structurally very similar, but differ substantially in thermal stability.
Probab=31.09 E-value=3.6e+02 Score=23.57 Aligned_cols=137 Identities=14% Similarity=0.116 Sum_probs=68.2
Q ss_pred ccHhHHHHHHHHHHhCCCeEEecCCCCCCCccccCCCCCCCCCCCCCCeEEEecCCc-ccHHHHH-hhCCCceEEEeCCC
Q 042576 47 QFASAIRAAKPELEKQGFKVMIPQSKPLSAGEVLGCTAPKIPARESDFNLVFIADGR-FHLEAFM-ISNPGIKTFRYDPY 124 (313)
Q Consensus 47 Qf~~~l~~~~~~L~~~g~~v~ipq~~pls~GevLGCt~~~~~~~~~~d~iv~igdGr-FHle~~m-i~np~~~~y~yDPy 124 (313)
-|...++.+.+.+++.|+.+++-.... .+.+...+-..... ..+|++++.+... .....+. +....+|++..|-.
T Consensus 13 ~~~~~~~~i~~~~~~~g~~v~~~~~~~-~~~~~~~~~~~~~~--~~~dgii~~~~~~~~~~~~l~~l~~~~ipvv~~~~~ 89 (268)
T cd06323 13 FFVTLKDGAQKEAKELGYELTVLDAQN-DAAKQLNDIEDLIT--RGVDAIIINPTDSDAVVPAVKAANEAGIPVFTIDRE 89 (268)
T ss_pred HHHHHHHHHHHHHHHcCceEEecCCCC-CHHHHHHHHHHHHH--cCCCEEEEcCCChHHHHHHHHHHHHCCCcEEEEccC
Confidence 445556778888888888876521110 01000000000001 1368887765321 1112222 23346777776543
Q ss_pred C---CcccccccChHHH-HHHHHHHHHHHhhcCCEEEEEEeCCCCCCcHHHHHHHHHHHHHc-CCcEE
Q 042576 125 L---GKLFLEEYDNKGM-RETRKRAIEKAMKEARTWGIVLGTLGRQGNPRILERLQKRMEKK-GFDYV 187 (313)
Q Consensus 125 s---~~~~~e~~d~~~~-l~~R~~~I~kak~~A~~~GIIvgTLg~Q~~~~ii~~l~~ll~~~-Gkk~y 187 (313)
. ..+.....|..+. ...=.++++... ..++++++.|.........-.+-.++.++++ |.+..
T Consensus 90 ~~~~~~~~~v~~d~~~~~~~~~~~l~~~~~-g~~~i~~l~~~~~~~~~~~r~~g~~~~l~~~~~~~~~ 156 (268)
T cd06323 90 ANGGEVVSQIASDNVAGGKMAAEYLVKLLG-GKGKVVELQGIPGASAARERGKGFHEVVDKYPGLKVV 156 (268)
T ss_pred CCCCceEEEEccCcHHHHHHHHHHHHHHhC-CCceEEEEeCCCCCccHHHHHHHHHHHHHhCCCcEEE
Confidence 2 1122233443322 111134445544 5678999988776655566667777888874 66644
No 204
>COG2984 ABC-type uncharacterized transport system, periplasmic component [General function prediction only]
Probab=31.09 E-value=1.4e+02 Score=29.44 Aligned_cols=48 Identities=21% Similarity=0.200 Sum_probs=40.8
Q ss_pred CChHHHHHHHHHhCCCCCeEEEEecccc---HhHHHHHHHHHHhCCCeEEe
Q 042576 21 IDVNRLIDTIKVNYSDPGKLILAGTIQF---ASAIRAAKPELEKQGFKVMI 68 (313)
Q Consensus 21 iD~~~~i~~i~~~f~~~~~i~Lv~tiQf---~~~l~~~~~~L~~~g~~v~i 68 (313)
.|++..++-+++.+|.-++|++++.--. ...++.++..++..|.+|+.
T Consensus 143 ~~v~q~i~lik~~~Pnak~Igv~Y~p~E~ns~~l~eelk~~A~~~Gl~vve 193 (322)
T COG2984 143 LPVAQQIELIKALLPNAKSIGVLYNPGEANSVSLVEELKKEARKAGLEVVE 193 (322)
T ss_pred chHHHHHHHHHHhCCCCeeEEEEeCCCCcccHHHHHHHHHHHHHCCCEEEE
Confidence 4577888999999999999999998877 66678899999999999763
No 205
>TIGR03029 EpsG chain length determinant protein tyrosine kinase EpsG. The proteins in this family are homologs of the EpsG protein found in Methylobacillus strain 12S and are generally found in operons with other Eps homologs. The protein is believed to function as the protein tyrosine kinase component of the chain length regulator (along with the transmembrane component EpsF).
Probab=31.06 E-value=3.3e+02 Score=24.95 Aligned_cols=56 Identities=18% Similarity=0.187 Sum_probs=40.1
Q ss_pred HHHHHHHHHHHHHhhcCCEEEEEEeCCCCCCcHHHHHHHHHHHHHcCCcEEEEEeC
Q 042576 137 GMRETRKRAIEKAMKEARTWGIVLGTLGRQGNPRILERLQKRMEKKGFDYVVIMMS 192 (313)
Q Consensus 137 ~~l~~R~~~I~kak~~A~~~GIIvgTLg~Q~~~~ii~~l~~ll~~~Gkk~y~i~v~ 192 (313)
.+...|..+......+..++=.|.|+.|+.|--.+.-.|-..+.+.|+++.+|=.+
T Consensus 86 ~~~~l~~~l~~~~~~~~~~vi~vts~~~g~Gktt~a~nLA~~la~~g~~VllID~D 141 (274)
T TIGR03029 86 ALRALRSQLMLRWFSEGRKALAVVSAKSGEGCSYIAANLAIVFSQLGEKTLLIDAN 141 (274)
T ss_pred HHHHHHHHhhhhccCCCCeEEEEECCCCCCCHHHHHHHHHHHHHhcCCeEEEEeCC
Confidence 34444544433322134455588999999999999999999999999998777554
No 206
>cd02036 MinD Bacterial cell division requires the formation of a septum at mid-cell. The site is determined by the min operon products MinC, MinD and MinE. MinC is a nonspecific inhibitor of the septum protein FtsZ. MinE is the supressor of MinC. MinD plays a pivotal role, selecting the mid-cell over other sites through the activation and regulation of MinC and MinE. MinD is a membrane-associated ATPase, related to nitrogenase iron protein. More distantly related proteins include flagellar biosynthesis proteins and ParA chromosome partitioning proteins. MinD is a monomer.
Probab=31.00 E-value=88 Score=26.21 Aligned_cols=60 Identities=20% Similarity=0.239 Sum_probs=43.0
Q ss_pred EEEeCCCCCCcHHHHHHHHHHHHHcCCcEEEEEeCC--CCHHHHhcCcC-------Ccc--EEEEecCCCc
Q 042576 158 IVLGTLGRQGNPRILERLQKRMEKKGFDYVVIMMSE--ISPARVALFED-------SVD--AWIQIACPRL 217 (313)
Q Consensus 158 IIvgTLg~Q~~~~ii~~l~~ll~~~Gkk~y~i~v~e--inp~KLanf~~-------~ID--~fV~iaCPrl 217 (313)
.|.+++||.|--.+.-+|-..|.++|+++.++=++- -+...+..... ++- =||++-||..
T Consensus 3 ~v~~~kgG~GKtt~a~~la~~l~~~g~~vllvD~D~~~~~~~~~~~~~~~~~~~~~~~~~~d~viiD~p~~ 73 (179)
T cd02036 3 VVTSGKGGVGKTTTTANLGTALAQLGYKVVLIDADLGLRNLDLILGLENRVVYTLHDVLAGDYILIDSPAG 73 (179)
T ss_pred EEeeCCCCCCHHHHHHHHHHHHHhCCCeEEEEeCCCCCCCchhhccccccCCcchhhcccCCEEEEECCCC
Confidence 578999999999999999999999999988886553 34444321110 111 3888889864
No 207
>cd05565 PTS_IIB_lactose PTS_IIB_lactose: subunit IIB of enzyme II (EII) of the lactose-specific phosphoenolpyruvate:carbohydrate phosphotransferase system (PTS) found in Firmicutes as well as Actinobacteria. In this system, EII is a lactose-specific permease with two cytoplasmic domains (IIA and IIB) and a transmembrane channel IIC domain. The IIC and IIB domains are expressed as a single protein from the lac operon. The IIB domain fold includes a central four-stranded parallel open twisted beta-sheet flanked by alpha-helices on both sides. The seven major PTS systems with this IIB fold include lactose, chitobiose/lichenan, ascorbate, galactitol, mannitol, fructose, and a sensory system with similarity to the bacterial bgl system.
Probab=30.98 E-value=1.4e+02 Score=24.06 Aligned_cols=55 Identities=18% Similarity=0.186 Sum_probs=35.5
Q ss_pred EEEeCCCCCCcHHHHHHHHHHHHHcCCcEEEEEeCCCCHHHHhcCcCCccEEEEecCCCcc
Q 042576 158 IVLGTLGRQGNPRILERLQKRMEKKGFDYVVIMMSEISPARVALFEDSVDAWIQIACPRLS 218 (313)
Q Consensus 158 IIvgTLg~Q~~~~ii~~l~~ll~~~Gkk~y~i~v~einp~KLanf~~~ID~fV~iaCPrls 218 (313)
+|+++-| --+--+++++++.++++|.++.+...+.-..+. +.+ ++|+++. =|+.+
T Consensus 4 ll~C~~G-aSSs~la~km~~~a~~~gi~~~i~a~~~~e~~~--~~~-~~Dvill--~PQv~ 58 (99)
T cd05565 4 LVLCAGG-GTSGLLANALNKGAKERGVPLEAAAGAYGSHYD--MIP-DYDLVIL--APQMA 58 (99)
T ss_pred EEECCCC-CCHHHHHHHHHHHHHHCCCcEEEEEeeHHHHHH--hcc-CCCEEEE--cChHH
Confidence 3455434 667779999999999999987766555443332 344 6885443 35543
No 208
>PRK10936 TMAO reductase system periplasmic protein TorT; Provisional
Probab=30.81 E-value=1.2e+02 Score=28.82 Aligned_cols=65 Identities=15% Similarity=0.005 Sum_probs=43.7
Q ss_pred HhhcCCEEEEEEeCCCCCCcHHHHHHHHHHHHHcCCcEEEEEeC-CCCHHHH----hcCc-CCccEEEEecC
Q 042576 149 AMKEARTWGIVLGTLGRQGNPRILERLQKRMEKKGFDYVVIMMS-EISPARV----ALFE-DSVDAWIQIAC 214 (313)
Q Consensus 149 ak~~A~~~GIIvgTLg~Q~~~~ii~~l~~ll~~~Gkk~y~i~v~-einp~KL----anf~-~~ID~fV~iaC 214 (313)
|+ ..++||+|+-++.-.....+++.+++.+++.|.+..++... +-+.++. .++- ..+|++|+.+.
T Consensus 43 Ar-~t~~Igvv~p~~~~~f~~~~~~gi~~aa~~~G~~l~i~~~~~~~~~~~q~~~i~~l~~~~vdgIIl~~~ 113 (343)
T PRK10936 43 AK-KAWKLCALYPHLKDSYWLSVNYGMVEEAKRLGVDLKVLEAGGYYNLAKQQQQLEQCVAWGADAILLGAV 113 (343)
T ss_pred cC-CCeEEEEEecCCCchHHHHHHHHHHHHHHHhCCEEEEEcCCCCCCHHHHHHHHHHHHHhCCCEEEEeCC
Confidence 35 56899999988877777788899999999999765554332 2333332 2221 14899988654
No 209
>PLN02948 phosphoribosylaminoimidazole carboxylase
Probab=30.76 E-value=1.6e+02 Score=31.03 Aligned_cols=98 Identities=14% Similarity=0.272 Sum_probs=63.8
Q ss_pred hhCCCceEEEeCC-CCCc------ccccccChHHHHHHHHHHHHHHhh-------cCCEEEEEEeCCCCCCcHHHHHHHH
Q 042576 111 ISNPGIKTFRYDP-YLGK------LFLEEYDNKGMRETRKRAIEKAMK-------EARTWGIVLGTLGRQGNPRILERLQ 176 (313)
Q Consensus 111 i~np~~~~y~yDP-ys~~------~~~e~~d~~~~l~~R~~~I~kak~-------~A~~~GIIvgTLg~Q~~~~ii~~l~ 176 (313)
+..|...+..|.. -++. ++...-+.++...+-..++..... ....+|||+|+ .-...+++...
T Consensus 354 ~~~p~~~v~~ygk~~~r~~rkmGhV~~~g~~~~e~~~~~~~~~~~~~~~~~~~~~~~~~v~i~~gs---~sd~~~~~~~~ 430 (577)
T PLN02948 354 LNIPGASVHWYGKPEMRKQRKMGHITVVGPSAAEVEARLDQLLAEESADPDALPKGTPLVGIIMGS---DSDLPTMKDAA 430 (577)
T ss_pred hhCCCCEEEEecCCCCCCCCeeEEEEEecCCHHHHHHHHHHHHhhhccCCCCCCCCCCeEEEEECc---hhhHHHHHHHH
Confidence 3457778888763 2221 111123444444444444433221 24579999988 67899999999
Q ss_pred HHHHHcCCcEEEEEeC-CCCHHHHhcC------cCCccEEEEe
Q 042576 177 KRMEKKGFDYVVIMMS-EISPARVALF------EDSVDAWIQI 212 (313)
Q Consensus 177 ~ll~~~Gkk~y~i~v~-einp~KLanf------~~~ID~fV~i 212 (313)
+.|++-|.++-+-+.| .=+|+++..| . ++++||.+
T Consensus 431 ~~l~~~g~~~~~~v~sahr~~~~~~~~~~~~~~~-~~~v~i~~ 472 (577)
T PLN02948 431 EILDSFGVPYEVTIVSAHRTPERMFSYARSAHSR-GLQVIIAG 472 (577)
T ss_pred HHHHHcCCCeEEEEECCccCHHHHHHHHHHHHHC-CCCEEEEE
Confidence 9999999998766665 5689999987 3 58887743
No 210
>TIGR00550 nadA quinolinate synthetase complex, A subunit. This protein, termed NadA, plays a role in the synthesis of pyridine, a precursor to NAD. The quinolinate synthetase complex consists of A protein (this protein) and B protein. B protein converts L-aspartate to iminoaspartate, an unstable reaction product which in the absence of A protein is spontaneously hydrolyzed to form oxaloacetate. The A protein, NadA, converts iminoaspartate to quinolate.
Probab=30.70 E-value=5.1e+02 Score=25.17 Aligned_cols=28 Identities=7% Similarity=0.045 Sum_probs=19.6
Q ss_pred CeEEEecCCcccHHHHHhhCCCceEEEeCC
Q 042576 94 FNLVFIADGRFHLEAFMISNPGIKTFRYDP 123 (313)
Q Consensus 94 d~iv~igdGrFHle~~mi~np~~~~y~yDP 123 (313)
+.|+|.+| +|-.+.++ .+|.+.++..|+
T Consensus 144 ~~Iif~pd-~~L~~~~~-~~p~k~~i~~~~ 171 (310)
T TIGR00550 144 KKILFLPD-KNLGRYVQ-EQTLKDMILWPE 171 (310)
T ss_pred CEEEEECc-hHHHHHHH-hCCCCEEEeCCC
Confidence 46777766 44455666 789999887743
No 211
>PF13964 Kelch_6: Kelch motif
Probab=30.67 E-value=51 Score=22.25 Aligned_cols=18 Identities=22% Similarity=0.132 Sum_probs=14.1
Q ss_pred CCCceEEEeCCCCCcccc
Q 042576 113 NPGIKTFRYDPYLGKLFL 130 (313)
Q Consensus 113 np~~~~y~yDPys~~~~~ 130 (313)
.+...+++|||.+++-+.
T Consensus 25 ~~~~~v~~yd~~t~~W~~ 42 (50)
T PF13964_consen 25 KYSNDVERYDPETNTWEQ 42 (50)
T ss_pred CccccEEEEcCCCCcEEE
Confidence 456789999999987653
No 212
>cd03821 GT1_Bme6_like This family is most closely related to the GT1 family of glycosyltransferases. Bme6 in Brucella melitensis has been shown to be involved in the biosynthesis of a polysaccharide.
Probab=30.55 E-value=1.3e+02 Score=27.21 Aligned_cols=54 Identities=13% Similarity=0.092 Sum_probs=30.5
Q ss_pred HHHHcCCcEEEEEeCCCCHHHHhcCcCCccEEEEecCCC---ccccccCCCCCcccC
Q 042576 178 RMEKKGFDYVVIMMSEISPARVALFEDSVDAWIQIACPR---LSIDWGDAFTKPLLT 231 (313)
Q Consensus 178 ll~~~Gkk~y~i~v~einp~KLanf~~~ID~fV~iaCPr---lsid~~~~f~kPvLT 231 (313)
++++.|....+.++|.++.+.+..+-...|++|+.+-.+ +++.+.-.+-+|+|+
T Consensus 254 ~~~~~~~~~~v~~~g~~~~~~~~~~~~~adv~v~ps~~e~~~~~~~Eama~G~PvI~ 310 (375)
T cd03821 254 IAAALGLEDRVTFTGMLYGEDKAAALADADLFVLPSHSENFGIVVAEALACGTPVVT 310 (375)
T ss_pred HHHhcCccceEEEcCCCChHHHHHHHhhCCEEEeccccCCCCcHHHHHHhcCCCEEE
Confidence 345556555666677777666554322688888766543 233344445555554
No 213
>cd02040 NifH NifH gene encodes component II (iron protein) of nitrogenase. Nitrogenase is responsible for the biological nitrogen fixation, i.e. reduction of molecular nitrogen to ammonia. NifH consists of two oxygen-sensitive metallosulfur proteins: the mollybdenum-iron (alternatively, vanadium-iron or iron-iron) protein (commonly referred to as component 1), and the iron protein (commonly referred to as component 2). The iron protein is a homodimer, with an Fe4S4 cluster bound between the subunits and two ATP-binding domains. It supplies energy by ATP hydrolysis, and transfers electrons from reduced ferredoxin or flavodoxin to component 1 for the reduction of molecular nitrogen to ammonia.
Probab=30.36 E-value=92 Score=28.32 Aligned_cols=36 Identities=19% Similarity=0.317 Sum_probs=30.5
Q ss_pred CEEEEEEeCCCCCCcHHHHHHHHHHHHHcCCcEEEEEe
Q 042576 154 RTWGIVLGTLGRQGNPRILERLQKRMEKKGFDYVVIMM 191 (313)
Q Consensus 154 ~~~GIIvgTLg~Q~~~~ii~~l~~ll~~~Gkk~y~i~v 191 (313)
++|.|. | +||-|-..+.-+|-..|.++|+++.+|=+
T Consensus 2 ~~iav~-~-KGGvGKTT~~~nLA~~La~~G~kVlliD~ 37 (270)
T cd02040 2 RQIAIY-G-KGGIGKSTTTQNLSAALAEMGKKVMIVGC 37 (270)
T ss_pred cEEEEE-e-CCcCCHHHHHHHHHHHHHhCCCeEEEEEc
Confidence 467776 6 99999999999999999999999877643
No 214
>PRK14095 pgi glucose-6-phosphate isomerase; Provisional
Probab=29.72 E-value=2.9e+02 Score=29.11 Aligned_cols=50 Identities=6% Similarity=0.033 Sum_probs=29.1
Q ss_pred cCCEEEEEEeCCCCCCcHHHHHH---HHHHHHHcCC--cEEEEEeCCCCHHHHhcCc
Q 042576 152 EARTWGIVLGTLGRQGNPRILER---LQKRMEKKGF--DYVVIMMSEISPARVALFE 203 (313)
Q Consensus 152 ~A~~~GIIvgTLg~Q~~~~ii~~---l~~ll~~~Gk--k~y~i~v~einp~KLanf~ 203 (313)
+.++.-+|+.++++ ...+.+.. +++.++++|. .-.++.++. +..+|+.|.
T Consensus 202 dpe~TLfiviSKSG-tT~ETl~n~~~~r~wl~~~G~~~~~h~VaVT~-~~s~l~~~~ 256 (533)
T PRK14095 202 DLAKTLFIVVSKSG-TTLETAANEEFVRDALKKAGLDYKKHFIAVTS-EGSPMDDES 256 (533)
T ss_pred CcccEEEEEEeCCC-CCHHHHHHHHHHHHHHHHcCccccceEEEEEC-CchHHHhhc
Confidence 45566677778776 44444443 4566776672 124445555 666677764
No 215
>TIGR01931 cysJ sulfite reductase [NADPH] flavoprotein, alpha-component. This model describes an NADPH-dependent sulfite reductase flavoprotein subunit. Most members of this family are found in Cys biosynthesis gene clusters. The closest homologs below the trusted cutoff are designated as subunits nitrate reductase.
Probab=29.71 E-value=1.1e+02 Score=32.19 Aligned_cols=51 Identities=16% Similarity=0.263 Sum_probs=42.2
Q ss_pred cCCEEEEEEeCCCCCCcHHHHHHHHHHHHHcCCcEEEEEeCCCCHHHHhcCc
Q 042576 152 EARTWGIVLGTLGRQGNPRILERLQKRMEKKGFDYVVIMMSEISPARVALFE 203 (313)
Q Consensus 152 ~A~~~GIIvgTLg~Q~~~~ii~~l~~ll~~~Gkk~y~i~v~einp~KLanf~ 203 (313)
.++.+.|+.||-.| +...+.++|.+.++++|..+.+.-|++..+..|....
T Consensus 57 ~~~~i~IlygSqTG-nae~~A~~l~~~l~~~g~~~~v~~~~d~~~~~l~~~~ 107 (597)
T TIGR01931 57 QEKRVTILYGSQTG-NARRLAKRLAEKLEAAGFSVRLSSADDYKFKQLKKER 107 (597)
T ss_pred CCCeEEEEEECCch-HHHHHHHHHHHHHHhCCCccEEechHHCCHhhcccCc
Confidence 45789999999753 3345999999999999999999999999988777654
No 216
>KOG3360 consensus Acylphosphatase [Energy production and conversion]
Probab=29.61 E-value=1e+02 Score=25.22 Aligned_cols=56 Identities=21% Similarity=0.299 Sum_probs=42.2
Q ss_pred HHHHHHHHHHhhcCCEEEEEEeCCCC------CCcHHHHHHHHHHHHHcCCcEEEEEeCCCCH
Q 042576 140 ETRKRAIEKAMKEARTWGIVLGTLGR------QGNPRILERLQKRMEKKGFDYVVIMMSEISP 196 (313)
Q Consensus 140 ~~R~~~I~kak~~A~~~GIIvgTLg~------Q~~~~ii~~l~~ll~~~Gkk~y~i~v~einp 196 (313)
--|..+..+|+ .....|-|..|--+ ||.++.++.+++.|...|-..-.|-=-|+++
T Consensus 22 ~fr~~t~~~a~-~lGlrGWv~Nt~~GtvkG~leGp~~~vd~mk~wl~~~gsP~s~I~~~ef~n 83 (98)
T KOG3360|consen 22 CFRKHTLDEAK-KLGLRGWVMNTSEGTVKGQLEGPPEKVDEMKEWLLTRGSPVSAIDRAEFSN 83 (98)
T ss_pred hhhHHHHHHHH-hhcceEEEEecCCceEEEEEeCCHHHHHHHHHHHHhcCChhHheeeeeecc
Confidence 44888999999 98888888877543 7999999999999999885544333333333
No 217
>COG0426 FpaA Uncharacterized flavoproteins [Energy production and conversion]
Probab=29.35 E-value=4.8e+02 Score=26.37 Aligned_cols=140 Identities=12% Similarity=0.165 Sum_probs=78.7
Q ss_pred ChHHHHHHHHH---hCCCCCeEEEEeccccHhH---HHHHHHHHHhCCCeEEecCCCCCCCccccCCCCCCCCCCCCCCe
Q 042576 22 DVNRLIDTIKV---NYSDPGKLILAGTIQFASA---IRAAKPELEKQGFKVMIPQSKPLSAGEVLGCTAPKIPARESDFN 95 (313)
Q Consensus 22 D~~~~i~~i~~---~f~~~~~i~Lv~tiQf~~~---l~~~~~~L~~~g~~v~ipq~~pls~GevLGCt~~~~~~~~~~d~ 95 (313)
++..+++...+ +.+.+ +|.|+++.-|-.. .+.+.+.|.+.|.+|.+-...-..++||+. +..+.++
T Consensus 229 ~~~~i~~~Y~~W~~~~~~~-~V~l~Y~smyg~T~~ma~aiaegl~~~gv~v~~~~~~~~~~~eI~~-------~i~~a~~ 300 (388)
T COG0426 229 NPKEIVEAYRDWAEGQPKG-KVDLIYDSMYGNTEKMAQAIAEGLMKEGVDVEVINLEDADPSEIVE-------EILDAKG 300 (388)
T ss_pred CHHHHHHHHHHHHccCCcc-eEEEEEecccCCHHHHHHHHHHHhhhcCCceEEEEcccCCHHHHHH-------HHhhcce
Confidence 45566666554 23333 7999998777655 577888888889887653322222333321 1112455
Q ss_pred EEEecCCcccHHHHHhhCCCceEEEeCCCCCcccccccChHHHHHHHHHHHHHHhhcCCEEEEEEeCCCCCCcHHHHHHH
Q 042576 96 LVFIADGRFHLEAFMISNPGIKTFRYDPYLGKLFLEEYDNKGMRETRKRAIEKAMKEARTWGIVLGTLGRQGNPRILERL 175 (313)
Q Consensus 96 iv~igdGrFHle~~mi~np~~~~y~yDPys~~~~~e~~d~~~~l~~R~~~I~kak~~A~~~GIIvgTLg~Q~~~~ii~~l 175 (313)
++ ||.-.. --+++. . +.-=...|...+ .-++-+.++|+-|..|- .++.|
T Consensus 301 ~v-vGsPT~---------------~~~~~p-----------~-i~~~l~~v~~~~-~~~k~~~vfgS~GW~g~--av~~i 349 (388)
T COG0426 301 LV-VGSPTI---------------NGGAHP-----------P-IQTALGYVLALA-PKNKLAGVFGSYGWSGE--AVDLI 349 (388)
T ss_pred EE-EecCcc---------------cCCCCc-----------h-HHHHHHHHHhcc-CcCceEEEEeccCCCCc--chHHH
Confidence 44 333211 001110 0 111123444555 66677899999998875 46889
Q ss_pred HHHHHHcCCcEEEE---EeCCCCHHHHh
Q 042576 176 QKRMEKKGFDYVVI---MMSEISPARVA 200 (313)
Q Consensus 176 ~~ll~~~Gkk~y~i---~v~einp~KLa 200 (313)
+++|+..|.+.-.- +-..++.+.|.
T Consensus 350 ~~~l~~~g~~~~~~~i~vk~~P~~~~l~ 377 (388)
T COG0426 350 EEKLKDLGFEFGFDGIEVKFRPTEEDLK 377 (388)
T ss_pred HHHHHhcCcEEeccceEEEecCCHHHHH
Confidence 99999999876433 33455555544
No 218
>cd00300 LDH_like L-lactate dehydrogenase-like enzymes. Members of this subfamily are tetrameric NAD-dependent 2-hydroxycarboxylate dehydrogenases including LDHs, L-2-hydroxyisocaproate dehydrogenases (L-HicDH), and LDH-like malate dehydrogenases (MDH). Dehydrogenases catalyze the conversion of carbonyl compounds to alcohols or amino acids. LDHs catalyze the last step of glycolysis in which pyruvate is converted to L-lactate. Vertebrate LDHs are non-allosteric, but some bacterial LDHs are activated by an allosteric effector such as fructose-1,6-bisphosphate. L-HicDH catalyzes the conversion of a variety of 2-oxo carboxylic acids with medium-sized aliphatic or aromatic side chains. MDH is one of the key enzymes in the citric acid cycle, facilitating both the conversion of malate to oxaloacetate and replenishing levels of oxalacetate by reductive carboxylation of pyruvate. The LDH-like subfamily is part of the NAD(P)-binding Rossmann fold superfamily, which includes a wide variety of prot
Probab=29.10 E-value=1.4e+02 Score=28.52 Aligned_cols=76 Identities=20% Similarity=0.170 Sum_probs=49.6
Q ss_pred eEEEeCCCCCcccccccChHHHHHH----HH---HHHHHHhhcCCEEEEEEeCCCCCC---------cHHHHHHHHHHHH
Q 042576 117 KTFRYDPYLGKLFLEEYDNKGMRET----RK---RAIEKAMKEARTWGIVLGTLGRQG---------NPRILERLQKRME 180 (313)
Q Consensus 117 ~~y~yDPys~~~~~e~~d~~~~l~~----R~---~~I~kak~~A~~~GIIvgTLg~Q~---------~~~ii~~l~~ll~ 180 (313)
.+..+|....+..-+..|...+... +. .-.+.++ +|..+=|..|+-...| +..+++.+-+.++
T Consensus 25 el~l~D~~~~~~~g~~~DL~~~~~~~~~~~i~~~~~~~~l~-~aDiVIitag~p~~~~~~R~~l~~~n~~i~~~~~~~i~ 103 (300)
T cd00300 25 ELVLVDVNEEKAKGDALDLSHASAFLATGTIVRGGDYADAA-DADIVVITAGAPRKPGETRLDLINRNAPILRSVITNLK 103 (300)
T ss_pred EEEEEeCCccHHHHHHHhHHHhccccCCCeEEECCCHHHhC-CCCEEEEcCCCCCCCCCCHHHHHHHHHHHHHHHHHHHH
Confidence 5888888665544433333322221 10 1135666 8888888888755444 6677888889999
Q ss_pred HcCCcEEEEEeCC
Q 042576 181 KKGFDYVVIMMSE 193 (313)
Q Consensus 181 ~~Gkk~y~i~v~e 193 (313)
+.+.+..+++++.
T Consensus 104 ~~~p~~~viv~sN 116 (300)
T cd00300 104 KYGPDAIILVVSN 116 (300)
T ss_pred HhCCCeEEEEccC
Confidence 9999999999885
No 219
>PRK11104 hemG protoporphyrinogen oxidase; Provisional
Probab=29.01 E-value=1.1e+02 Score=26.90 Aligned_cols=54 Identities=13% Similarity=0.204 Sum_probs=37.0
Q ss_pred EEEEEEeCCCCCCcHHHHHHHHHHHHHcCCcEEEEEeCCCCHHHHhcCcCCccEEEEecCC
Q 042576 155 TWGIVLGTLGRQGNPRILERLQKRMEKKGFDYVVIMMSEISPARVALFEDSVDAWIQIACP 215 (313)
Q Consensus 155 ~~GIIvgTLg~Q~~~~ii~~l~~ll~~~Gkk~y~i~v~einp~KLanf~~~ID~fV~iaCP 215 (313)
++.||-+|.. -....+++.|.+.|.. |..+-++-+.+.... ++. +.|+ |++++|
T Consensus 2 kilIvY~S~~-G~T~~iA~~Ia~~l~~-g~~v~~~~~~~~~~~---~l~-~yD~-vIlGsp 55 (177)
T PRK11104 2 KTLILYSSRD-GQTRKIASYIASELKE-GIQCDVVNLHRIEEP---DLS-DYDR-VVIGAS 55 (177)
T ss_pred cEEEEEECCC-ChHHHHHHHHHHHhCC-CCeEEEEEhhhcCcc---CHH-HCCE-EEEECc
Confidence 4678888854 2344678999999987 887777777765543 344 4677 666666
No 220
>PRK13055 putative lipid kinase; Reviewed
Probab=28.91 E-value=2.4e+02 Score=27.18 Aligned_cols=38 Identities=8% Similarity=0.178 Sum_probs=24.6
Q ss_pred CEEEEEEeCCCCCCc-HHHHHHHHHHHHHcCCcEEEEEe
Q 042576 154 RTWGIVLGTLGRQGN-PRILERLQKRMEKKGFDYVVIMM 191 (313)
Q Consensus 154 ~~~GIIvgTLg~Q~~-~~ii~~l~~ll~~~Gkk~y~i~v 191 (313)
+++.||++..++.+. ...++++++.|+++|.++-++..
T Consensus 3 ~r~~iI~NP~sG~~~~~~~~~~i~~~l~~~g~~~~i~~t 41 (334)
T PRK13055 3 KRARLIYNPTSGQEIMKKNVADILDILEQAGYETSAFQT 41 (334)
T ss_pred ceEEEEECCCCCchhHHHHHHHHHHHHHHcCCeEEEEEe
Confidence 356677777776665 45667777777777766554444
No 221
>cd06354 PBP1_BmpA_PnrA_like Periplasmic binding domain of basic membrane lipoprotein, PnrA, in Treponema pallidum and its homologs from other bacteria and Archaea. Periplasmic binding domain of basic membrane lipoprotein, PnrA, in Treponema pallidum and its homologs from other bacteria and Archaea. The PnrA lipoprotein, also known as Tp0319 or TmpC, represents a novel family of bacterial purine nucleoside receptor encoded within an ATP-binding cassette (ABC) transport system (pnrABCDE). It shows a striking structural similarity to another basic membrane lipoprotein Med which regulates the competence transcription factor gene, comK, in Bacillus subtilis. The members of PnrA-like subgroup are likely to have similar nucleoside-binding functions and a similar type I periplasmic sugar-binding protein-like fold.
Probab=28.88 E-value=1.5e+02 Score=26.81 Aligned_cols=14 Identities=21% Similarity=0.356 Sum_probs=5.8
Q ss_pred HHHHHHHHHHHHcC
Q 042576 170 RILERLQKRMEKKG 183 (313)
Q Consensus 170 ~ii~~l~~ll~~~G 183 (313)
.+++.+++.+++.|
T Consensus 19 ~~~~gi~~~~~~~g 32 (265)
T cd06354 19 SAWEGLERAAKELG 32 (265)
T ss_pred HHHHHHHHHHHHcC
Confidence 34444444444444
No 222
>cd06325 PBP1_ABC_uncharacterized_transporter Type I periplasmic ligand-binding domain of uncharacterized ABC-type transport systems that are predicted to be involved in the uptake of amino acids, peptides, or inorganic ions. This group includes the type I periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type transport systems that are predicted to be involved in the uptake of amino acids, peptides, or inorganic ions. This subgroup has high sequence similarity to members of the family of hydrophobic amino acid transporters (HAAT), such as leucine/isoleucine/valine binding protein (LIVBP); its ligand specificity has not been determined experimentally.
Probab=28.34 E-value=1.6e+02 Score=26.21 Aligned_cols=58 Identities=12% Similarity=0.168 Sum_probs=33.5
Q ss_pred EEEEEEeCCCCCCcHHHHHHHHHHHHHcCC----cEEEEEeC-CCCHH-------HHhcCcCCccEEEEecCC
Q 042576 155 TWGIVLGTLGRQGNPRILERLQKRMEKKGF----DYVVIMMS-EISPA-------RVALFEDSVDAWIQIACP 215 (313)
Q Consensus 155 ~~GIIvgTLg~Q~~~~ii~~l~~ll~~~Gk----k~y~i~v~-einp~-------KLanf~~~ID~fV~iaCP 215 (313)
+||+++. ..-..+..+++.+++.++++|. +..+++.+ +-+++ +|.+- .+|++|..+++
T Consensus 1 ~igv~~~-~~~~~~~~~~~gi~~~~~~~g~~~g~~v~l~~~~~~~~~~~~~~~~~~l~~~--~vd~iI~~~~~ 70 (281)
T cd06325 1 KVGILQL-VEHPALDAARKGFKDGLKEAGYKEGKNVKIDYQNAQGDQSNLPTIARKFVAD--KPDLIVAIATP 70 (281)
T ss_pred CeEEecC-CCCcchHHHHHHHHHHHHHhCccCCceEEEEEecCCCCHHHHHHHHHHHHhc--CCCEEEEcCcH
Confidence 4677774 5555666778888888888775 23333332 22333 33332 47777776653
No 223
>PRK10401 DNA-binding transcriptional regulator GalS; Provisional
Probab=28.32 E-value=5e+02 Score=24.27 Aligned_cols=140 Identities=11% Similarity=0.007 Sum_probs=66.7
Q ss_pred eEEEEe-c---cccHhHHHHHHHHHHhCCCeEEecCCCCCCCccccCCCCCCCCCCCCCCeEEEecCCcccHHHHHhhCC
Q 042576 39 KLILAG-T---IQFASAIRAAKPELEKQGFKVMIPQSKPLSAGEVLGCTAPKIPARESDFNLVFIADGRFHLEAFMISNP 114 (313)
Q Consensus 39 ~i~Lv~-t---iQf~~~l~~~~~~L~~~g~~v~ipq~~pls~GevLGCt~~~~~~~~~~d~iv~igdGrFHle~~mi~np 114 (313)
.|+++. + --|...++.+.+.+++.|+.+++..... .+.+....- ..+.. ..+|++|+.+.......-..+..
T Consensus 61 ~Igvi~~~~~~~f~~~l~~gi~~~~~~~gy~~~~~~~~~-~~~~~~~~i-~~l~~-~~vdGiIi~~~~~~~~~~~~~~~- 136 (346)
T PRK10401 61 TIGVVVMDVSDAFFGALVKAVDLVAQQHQKYVLIGNSYH-EAEKERHAI-EVLIR-QRCNALIVHSKALSDDELAQFMD- 136 (346)
T ss_pred EEEEEeCCCCCccHHHHHHHHHHHHHHCCCEEEEEcCCC-ChHHHHHHH-HHHHh-cCCCEEEEeCCCCChHHHHHHHh-
Confidence 477663 2 2355567788889999999976522110 000000000 00001 23789888764322211111221
Q ss_pred Cce-EEEeCCCC--CcccccccChHHH--HHHHHHHHHHHhhcCCEEEEEEeCCCCCCcHHHHHHHHHHHHHcCCcE
Q 042576 115 GIK-TFRYDPYL--GKLFLEEYDNKGM--RETRKRAIEKAMKEARTWGIVLGTLGRQGNPRILERLQKRMEKKGFDY 186 (313)
Q Consensus 115 ~~~-~y~yDPys--~~~~~e~~d~~~~--l~~R~~~I~kak~~A~~~GIIvgTLg~Q~~~~ii~~l~~ll~~~Gkk~ 186 (313)
..+ ++.+|-.. ..+.....|.... ...++ ++ .+ ..+++|+|.|.........-.+-.++-++++|...
T Consensus 137 ~~p~vV~i~~~~~~~~~~~V~~D~~~~~~~a~~~-L~--~~-G~~~I~~i~~~~~~~~~~~R~~Gf~~al~~~gi~~ 209 (346)
T PRK10401 137 QIPGMVLINRVVPGYAHRCVCLDNVSGARMATRM-LL--NN-GHQRIGYLSSSHGIEDDAMRRAGWMSALKEQGIIP 209 (346)
T ss_pred cCCCEEEEecccCCCCCCEEEECcHHHHHHHHHH-HH--HC-CCCeEEEEeCCCcCcchHHHHHHHHHHHHHcCCCC
Confidence 233 55555221 1111122333221 11111 11 23 66899999877554444455566778888888653
No 224
>PF02593 dTMP_synthase: Thymidylate synthase; InterPro: IPR003745 This entry describes proteins of unknown function.
Probab=28.16 E-value=94 Score=28.80 Aligned_cols=41 Identities=22% Similarity=0.310 Sum_probs=32.2
Q ss_pred HHHHHHHhhcCCEEEEEEeCCCCCCcHHHHHHHHHHHHHcCCcE
Q 042576 143 KRAIEKAMKEARTWGIVLGTLGRQGNPRILERLQKRMEKKGFDY 186 (313)
Q Consensus 143 ~~~I~kak~~A~~~GIIvgTLg~Q~~~~ii~~l~~ll~~~Gkk~ 186 (313)
+.++++|+ +++.=+||+++-... +.+.+.|++.+++.|..+
T Consensus 66 ~~l~~~~~-e~g~kavIvp~~~~~--~g~~~~lk~~~e~~gi~~ 106 (217)
T PF02593_consen 66 YELPEIAK-EAGVKAVIVPSESPK--PGLRRQLKKQLEEFGIEV 106 (217)
T ss_pred HHHHHHHH-HcCCCEEEEecCCCc--cchHHHHHHHHHhcCcee
Confidence 45677888 778888888887666 888899999999877554
No 225
>cd06317 PBP1_ABC_sugar_binding_like_8 Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems. Pperiplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily, which consists of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis.
Probab=28.14 E-value=1.2e+02 Score=26.90 Aligned_cols=30 Identities=13% Similarity=0.197 Sum_probs=13.2
Q ss_pred EEEEEeCC-CCCCcHHHHHHHHHHHHHcCCc
Q 042576 156 WGIVLGTL-GRQGNPRILERLQKRMEKKGFD 185 (313)
Q Consensus 156 ~GIIvgTL-g~Q~~~~ii~~l~~ll~~~Gkk 185 (313)
||+|+-++ .......+++.+++.++++|..
T Consensus 2 i~vi~p~~~~~~~~~~~~~g~~~~~~~~g~~ 32 (275)
T cd06317 2 IGYTQNNVGSHSYQTTYNKAFQAAAEEDGVE 32 (275)
T ss_pred eEEEecccCCCHHHHHHHHHHHHHHHhcCCE
Confidence 44444443 3333334444444444444444
No 226
>cd06321 PBP1_ABC_sugar_binding_like_11 Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems. This group includes the periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily, which consist of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis.
Probab=27.56 E-value=1.7e+02 Score=25.99 Aligned_cols=30 Identities=17% Similarity=0.168 Sum_probs=17.8
Q ss_pred EEEEEeCCCCCCcHHHHHHHHHHHHHcCCc
Q 042576 156 WGIVLGTLGRQGNPRILERLQKRMEKKGFD 185 (313)
Q Consensus 156 ~GIIvgTLg~Q~~~~ii~~l~~ll~~~Gkk 185 (313)
||+|+.++.--....+++.+++.+++.|..
T Consensus 2 Ig~v~~~~~~~~~~~~~~gi~~~~~~~~~~ 31 (271)
T cd06321 2 IGVSVGDLGNPFFVALAKGAEAAAKKLNPG 31 (271)
T ss_pred eEEEecccCCHHHHHHHHHHHHHHHHhCCC
Confidence 566666665555556666666666664333
No 227
>PRK13185 chlL protochlorophyllide reductase iron-sulfur ATP-binding protein; Provisional
Probab=27.54 E-value=1.1e+02 Score=28.18 Aligned_cols=37 Identities=22% Similarity=0.219 Sum_probs=31.2
Q ss_pred CCEEEEEEeCCCCCCcHHHHHHHHHHHHHcCCcEEEEEe
Q 042576 153 ARTWGIVLGTLGRQGNPRILERLQKRMEKKGFDYVVIMM 191 (313)
Q Consensus 153 A~~~GIIvgTLg~Q~~~~ii~~l~~ll~~~Gkk~y~i~v 191 (313)
++++.|. | +||-|--.+.-+|-..|.++||++.+|=+
T Consensus 2 ~~iIav~-~-KGGVGKTT~~~nLA~~la~~G~kVLliD~ 38 (270)
T PRK13185 2 ALVLAVY-G-KGGIGKSTTSSNLSAAFAKLGKKVLQIGC 38 (270)
T ss_pred ceEEEEE-C-CCCCCHHHHHHHHHHHHHHCCCeEEEEec
Confidence 4677776 6 99999999999999999999999776633
No 228
>cd03466 Nitrogenase_NifN_2 Nitrogenase_nifN_2: A subgroup of the NifN subunit of the NifEN complex: NifN forms an alpha2beta2 tetramer with NifE. NifN and nifE are structurally homologous to nitrogenase MoFe protein beta and alpha subunits respectively. NifEN participates in the synthesis of the iron-molybdenum cofactor (FeMoco) of the MoFe protein. NifB-co (an iron and sulfur containing precursor of the FeMoco) from NifB is transferred to the NifEN complex where it is further processed to FeMoco. The nifEN bound precursor of FeMoco has been identified as a molybdenum-free, iron- and sulfur- containing analog of FeMoco. It has been suggested that this nifEN bound precursor also acts as a cofactor precursor in nitrogenase systems which require a cofactor other than FeMoco: i.e. iron-vanadium cofactor (FeVco) or iron only cofactor (FeFeco). This group also contains the Clostidium fused NifN-NifB protein.
Probab=27.30 E-value=6.4e+02 Score=25.23 Aligned_cols=183 Identities=16% Similarity=0.152 Sum_probs=90.2
Q ss_pred CCcCEEEEcccccC-C----hHHHHHHHHHhCC----CCCeEEEEeccccHhHHHHHHHHHHhCCCeEE-ecCCCCCCCc
Q 042576 8 TRIPCLYVFVEIKI-D----VNRLIDTIKVNYS----DPGKLILAGTIQFASAIRAAKPELEKQGFKVM-IPQSKPLSAG 77 (313)
Q Consensus 8 t~ipvlYVFv~i~i-D----~~~~i~~i~~~f~----~~~~i~Lv~tiQf~~~l~~~~~~L~~~g~~v~-ipq~~pls~G 77 (313)
..+||++|-..-.- + .+..++.+.+++. +..+|.|++.......+..+++.|++-|.+++ +|...-..+|
T Consensus 117 ~~~~vi~v~t~gF~g~~~~G~~~a~~al~~~~~~~~~~~~~VNlig~~~~~~D~~ei~~lL~~~Gl~~~~~~d~s~~~~~ 196 (429)
T cd03466 117 SEPKIIPASTPGYGGTHVEGYDTAVRSIVKNIAVDPDKIEKINVIAGMMSPADIREIKEILREFGIEYILLPDTSETLDG 196 (429)
T ss_pred CCCcEEEEECCCCcccHHHHHHHHHHHHHHHhccCCCCCCcEEEECCCCChhHHHHHHHHHHHcCCCeEEecCccccccC
Confidence 36788887553221 1 1234455544442 23458888765566678999999999998864 3543322333
Q ss_pred ccc---------CCCCCCCCCCCCCCeEEEecC--Ccc-cHHHHHhhCCCceEEEeC-CCCCcccccc---------cC-
Q 042576 78 EVL---------GCTAPKIPARESDFNLVFIAD--GRF-HLEAFMISNPGIKTFRYD-PYLGKLFLEE---------YD- 134 (313)
Q Consensus 78 evL---------GCt~~~~~~~~~~d~iv~igd--GrF-Hle~~mi~np~~~~y~yD-Pys~~~~~e~---------~d- 134 (313)
... |++...+..-.+...-+.++. +.. -+-..|=..-++|.+.++ |+.-+-|..- .+
T Consensus 197 ~~~~~~~~~~~~g~~~~~i~~~~~A~lniv~~~~~~~g~~~A~~L~e~~giP~~~~~~P~G~~~t~~~l~~l~~~~g~~~ 276 (429)
T cd03466 197 PFWGEYHRLPSGGTPISEIKGMGGAKATIELGMFVDHGLSAGSYLEEEFGIPNYRLPLPIGLRATDEFMSLLSKLTGKPI 276 (429)
T ss_pred CCCCCcceeCCCCCCHHHHHhhccCcEEEEEccCccchHHHHHHHHHHHCCCeeecCCCcChHHHHHHHHHHHHHHCCCc
Confidence 332 222221211111334344542 111 122233233467776665 3421111100 00
Q ss_pred hHHHHHHHHHHHH---HHhh--cCCEEEEEEeCCCCCCcHHHHHHHHHHHHHcCCcEEEEEeCCCCHH
Q 042576 135 NKGMRETRKRAIE---KAMK--EARTWGIVLGTLGRQGNPRILERLQKRMEKKGFDYVVIMMSEISPA 197 (313)
Q Consensus 135 ~~~~l~~R~~~I~---kak~--~A~~~GIIvgTLg~Q~~~~ii~~l~~ll~~~Gkk~y~i~v~einp~ 197 (313)
.+.+.+.|...+. .+.. ..+++.|+ | .+..+-.|.+.|.+.|.+...+..+..++.
T Consensus 277 ~~~i~~~~~~~~~~~~d~~~~l~gkrv~v~-g------~~~~~~~l~~~L~elG~~~~~v~~~~~~~~ 337 (429)
T cd03466 277 PEKYTRERGRLLDAMIDAHKYNFGRKAAIY-G------EPDFVVAITRFVLENGMVPVLIATGSESKK 337 (429)
T ss_pred CHHHHHHHHHHHHHHHHHHHhcCCCEEEEE-c------CHHHHHHHHHHHHHCCCEEEEEEeCCCChH
Confidence 1223333333332 2210 23455433 3 356667778888889999877777665544
No 229
>TIGR02363 dhaK1 dihydroxyacetone kinase, DhaK subunit. Two types of dihydroxyacetone kinase (glycerone kinase) are described. In yeast and a few bacteria, e.g. Citrobacter freundii, the enzyme is a single chain that uses ATP as phosphoryl donor and is designated EC 2.7.1.29. By contract, E. coli and many other bacterial species have a multisubunit form (EC 2.7.1.-) with a phosphoprotein donor related to PTS transport proteins. This family represents the DhaK subunit of the latter type of dihydroxyacetone kinase, but it specifically excludes the DhaK paralog DhaK2 (TIGR02362) found in the same operon as DhaK and DhaK in the Firmicutes.
Probab=27.30 E-value=1.8e+02 Score=28.73 Aligned_cols=45 Identities=9% Similarity=0.206 Sum_probs=39.1
Q ss_pred cCCEEEEEEeCCCCCCcHH---HHHHHHHHHHHcCCcEEEEEeCCCCH
Q 042576 152 EARTWGIVLGTLGRQGNPR---ILERLQKRMEKKGFDYVVIMMSEISP 196 (313)
Q Consensus 152 ~A~~~GIIvgTLg~Q~~~~---ii~~l~~ll~~~Gkk~y~i~v~einp 196 (313)
+...+.++|+.||+--+++ +.+++.++|+++|.+.+.+.+|..-.
T Consensus 251 ~gd~v~vlvN~LG~ts~lEl~i~~~~v~~~L~~~gi~v~r~~vG~~~T 298 (329)
T TIGR02363 251 SGDRVIVLVNGMGATPLMELYIFYNDVQRLLEQRGVNVARTLVGNYMT 298 (329)
T ss_pred CCCeEEEEEeCCCCCCHHHHHHHHHHHHHHHHHCCCEEEEEEeecccc
Confidence 5668999999999999998 57889999999999999998887543
No 230
>PF01976 DUF116: Protein of unknown function DUF116; InterPro: IPR002829 These archaeal and bacterial proteins have no known function. Members of this family contain seven conserved cysteines and may also be an integral membrane protein.
Probab=27.18 E-value=60 Score=28.43 Aligned_cols=47 Identities=21% Similarity=0.280 Sum_probs=36.4
Q ss_pred HHHHHHHHHHHHHcCCcEEEEEeCCCCHHHHhcCcCCccEEEEecCCCc
Q 042576 169 PRILERLQKRMEKKGFDYVVIMMSEISPARVALFEDSVDAWIQIACPRL 217 (313)
Q Consensus 169 ~~ii~~l~~ll~~~Gkk~y~i~v~einp~KLanf~~~ID~fV~iaCPrl 217 (313)
.-.+..|.++.++.|.++|++.=|.+=..-+.... .|+.|-+||.|.
T Consensus 72 ~C~Ig~l~~lae~~g~~v~i~~Ggt~ar~~ik~~~--p~~iigVAC~~d 118 (158)
T PF01976_consen 72 KCDIGDLKKLAEKYGYKVYIATGGTLARKIIKEYR--PKAIIGVACERD 118 (158)
T ss_pred CCchhHHHHHHHHcCCEEEEEcChHHHHHHHHHhC--CCEEEEEechHH
Confidence 44567889999999999777776666555566665 789999999994
No 231
>cd03798 GT1_wlbH_like This family is most closely related to the GT1 family of glycosyltransferases. wlbH in Bordetella parapertussis has been shown to be required for the biosynthesis of a trisaccharide that, when attached to the B. pertussis lipopolysaccharide (LPS) core (band B), generates band A LPS.
Probab=27.17 E-value=41 Score=30.18 Aligned_cols=60 Identities=15% Similarity=0.218 Sum_probs=37.9
Q ss_pred HHHHHHHHHcCCcEEEEEeCCCCHHHHhcCcCCccEEEEecCCC---ccccccCCCCCcccCH
Q 042576 173 ERLQKRMEKKGFDYVVIMMSEISPARVALFEDSVDAWIQIACPR---LSIDWGDAFTKPLLTP 232 (313)
Q Consensus 173 ~~l~~ll~~~Gkk~y~i~v~einp~KLanf~~~ID~fV~iaCPr---lsid~~~~f~kPvLTP 232 (313)
+.+++++++.+....+.+++.++.++|..+-...|+++..+..+ +++.+.-.+.+|+|++
T Consensus 246 ~~~~~~~~~~~~~~~v~~~g~~~~~~~~~~~~~ad~~i~~~~~~~~~~~~~Ea~~~G~pvI~~ 308 (377)
T cd03798 246 EALEALAAELGLEDRVTFLGAVPHEEVPAYYAAADVFVLPSLREGFGLVLLEAMACGLPVVAT 308 (377)
T ss_pred HHHHHHHHhcCCcceEEEeCCCCHHHHHHHHHhcCeeecchhhccCChHHHHHHhcCCCEEEe
Confidence 45666666667667777888888888775532678888655432 2333444566666643
No 232
>PF09861 DUF2088: Domain of unknown function (DUF2088); InterPro: IPR018657 This domain, found in various hypothetical proteins, has no known function. ; PDB: 2YJG_B.
Probab=27.14 E-value=97 Score=28.22 Aligned_cols=35 Identities=23% Similarity=0.208 Sum_probs=25.0
Q ss_pred HHhhcCCEEEEEE--eCCCCCCcHHHHHHHHHHHHHcCC
Q 042576 148 KAMKEARTWGIVL--GTLGRQGNPRILERLQKRMEKKGF 184 (313)
Q Consensus 148 kak~~A~~~GIIv--gTLg~Q~~~~ii~~l~~ll~~~Gk 184 (313)
.++ ..+++.|++ +|.+ +.+..++..|-+.|+++|.
T Consensus 50 ~~~-~~~~V~Ivv~D~TRp-~p~~~il~~ll~~L~~~Gv 86 (204)
T PF09861_consen 50 LVK-PGKRVAIVVDDITRP-TPSDLILPALLEELEEAGV 86 (204)
T ss_dssp HCT-T-SEEEEEEE-TTS----HHHHHHHHHHHHHT-T-
T ss_pred HhC-CCCeEEEEeCCCCCC-CCHHHHHHHHHHHHHhcCC
Confidence 345 678999999 7777 7777899999999999887
No 233
>cd01538 PBP1_ABC_xylose_binding Periplasmic xylose-binding component of the ABC-type transport systems that belong to a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein (PBP1) superfamily. Periplasmic xylose-binding component of the ABC-type transport systems that belong to a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein (PBP1) superfamily, which consists of two alpha/beta globular domains connected by a three-stranded hinge. This Venus flytrap-like domain undergoes a transition from an open to a closed conformational state upon ligand binding. Moreover, the periplasmic xylose-binding protein is homologous to the ligand-binding domain of eukaryotic receptors such as glutamate receptor (GluR) and DNA-binding transcriptional repressors such as LacI and GalR.
Probab=27.04 E-value=4.7e+02 Score=23.68 Aligned_cols=129 Identities=11% Similarity=0.137 Sum_probs=60.2
Q ss_pred ccHhHHHHHHHHHHhCCCeEEecCC--CCCCCccccCCCCCCCCCCCCCCeEEEecC-CcccHHHH-HhhCCCceEEEeC
Q 042576 47 QFASAIRAAKPELEKQGFKVMIPQS--KPLSAGEVLGCTAPKIPARESDFNLVFIAD-GRFHLEAF-MISNPGIKTFRYD 122 (313)
Q Consensus 47 Qf~~~l~~~~~~L~~~g~~v~ipq~--~pls~GevLGCt~~~~~~~~~~d~iv~igd-GrFHle~~-mi~np~~~~y~yD 122 (313)
-|...++.+.+.+++.|+++.+-.. .+-...+.+- ..+. ..+|++++.+. +......+ .+....+|+..+|
T Consensus 13 ~~~~~~~gi~~~a~~~g~~~~~~~~~~~~~~~~~~i~---~~~~--~~vdgiii~~~~~~~~~~~l~~l~~~~ipvV~~~ 87 (288)
T cd01538 13 RWIRDRPNFEAALKELGAEVIVQNANGDPAKQISQIE---NMIA--KGVDVLVIAPVDGEALASAVEKAADAGIPVIAYD 87 (288)
T ss_pred HHHHHHHHHHHHHHHcCCEEEEECCCCCHHHHHHHHH---HHHH--cCCCEEEEecCChhhHHHHHHHHHHCCCCEEEEC
Confidence 3555567778888888888665211 0000000000 0011 23788877652 22111111 2233467887777
Q ss_pred CCCCc------ccccccChHHHHHHHHHHHHHH----hhcCCEEEEEEeCCCCCCcHHHHHHHHHHHHHcC
Q 042576 123 PYLGK------LFLEEYDNKGMRETRKRAIEKA----MKEARTWGIVLGTLGRQGNPRILERLQKRMEKKG 183 (313)
Q Consensus 123 Pys~~------~~~e~~d~~~~l~~R~~~I~ka----k~~A~~~GIIvgTLg~Q~~~~ii~~l~~ll~~~G 183 (313)
..... +....+...+... ..++++. . ..++++++.|+........-.+-+++-++++|
T Consensus 88 ~~~~~~~~~~~v~~d~~~~g~~~~--~~l~~~~~~~~~-g~~~i~~l~g~~~~~~~~~R~~gf~~~l~~~~ 155 (288)
T cd01538 88 RLILNSNVDYYVSFDNEKVGELQG--QALVDGLGAKGK-PPGNIELIAGSPTDNNAKLFFNGAMSVLKPLI 155 (288)
T ss_pred CCCCCCCcceEEEeChHHHHHHHH--HHHHHHHhhcCC-CCceEEEEECCCCCchHHHHHHHHHHHHHhcc
Confidence 43211 1111111222222 2233332 2 45678888887654333344455577777776
No 234
>TIGR01752 flav_long flavodoxin, long chain. Flavodoxins are small redox-active proteins with a flavin mononucleotide (FMN) prosthetic group. They can act in nitrogen fixation by nitrogenase, in sulfite reduction, and light-dependent NADP+ reduction in during photosynthesis, among other roles. This model describes the long chain type, typical for nitrogen fixation but associated with pyruvate formate-lyase activation and cobalamin-dependent methionine synthase activity in E. coli.
Probab=26.93 E-value=1.7e+02 Score=25.22 Aligned_cols=53 Identities=26% Similarity=0.370 Sum_probs=35.2
Q ss_pred EEEEEEeCCCCCCcHHHHHHHHHHHHHcCCcEEEEEeCCCCHHHHhcCcCCccEEEEecCC
Q 042576 155 TWGIVLGTLGRQGNPRILERLQKRMEKKGFDYVVIMMSEISPARVALFEDSVDAWIQIACP 215 (313)
Q Consensus 155 ~~GIIvgTLg~Q~~~~ii~~l~~ll~~~Gkk~y~i~v~einp~KLanf~~~ID~fV~iaCP 215 (313)
+++|+-+| ..-+...++++|.+.|.. ..+-++-+.+.+++.|.+ .|.++ +++|
T Consensus 1 ~i~IiY~S-~tGnTe~vA~~Ia~~l~~--~~~~i~~~~~~~~~~l~~----~d~ii-~gsp 53 (167)
T TIGR01752 1 KIGIFYGT-DTGNTEGIAEKIQKELGE--DDVDVFNIAKASKEDLNA----YDKLI-LGTP 53 (167)
T ss_pred CEEEEEEC-CCChHHHHHHHHHHHhCC--CceEEEEcccCCHhHHhh----CCEEE-EEec
Confidence 36888888 334455688999888864 346677788888766654 45544 4444
No 235
>cd01540 PBP1_arabinose_binding Periplasmic L-arabinose-binding protein (ABP), a member of a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily. Periplasmic L-arabinose-binding protein (ABP), a member of a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily. ABP is only involved in transport contrary to other related sugar-binding proteins such as the glucose/galactose-binding protein (GGBP) and the ribose-binding protein (RBP), both of which are involved in chemotaxis as well as transport. The periplasmic ABP consists of two alpha/beta globular domains connected by a three-stranded hinge, a Venus flytrap-like domain, which undergoes a transition from an open to a closed conformational state upon ligand binding. Moreover, ABP is homologous to the ligand-binding domain of eukaryotic receptors such as metabotropic glutamate receptor (mGluR) and DNA-binding transcriptional repressors such a
Probab=26.87 E-value=4.6e+02 Score=23.43 Aligned_cols=135 Identities=13% Similarity=0.107 Sum_probs=60.8
Q ss_pred cHhHHHHHHHHHHhCCCeEEecCCCCCCCccccCCCCCCCCCCCCCCeEEEecCC-cccHHHHH-hhCCCceEEEeCCCC
Q 042576 48 FASAIRAAKPELEKQGFKVMIPQSKPLSAGEVLGCTAPKIPARESDFNLVFIADG-RFHLEAFM-ISNPGIKTFRYDPYL 125 (313)
Q Consensus 48 f~~~l~~~~~~L~~~g~~v~ipq~~pls~GevLGCt~~~~~~~~~~d~iv~igdG-rFHle~~m-i~np~~~~y~yDPys 125 (313)
|...++.+.+.+++.|+++++-... .+.+....--.... ..+|++++.+.. ......+. +....+|++.+|-..
T Consensus 14 ~~~~~~gi~~~~~~~g~~~~~~~~~--~~~~~~~~i~~~~~--~~~dgiii~~~~~~~~~~~~~~~~~~~iPvV~~~~~~ 89 (289)
T cd01540 14 FQTEWKFAKKAAKEKGFTVVKIDVP--DGEKVLSAIDNLGA--QGAKGFVICVPDVKLGPAIVAKAKAYNMKVVAVDDRL 89 (289)
T ss_pred HHHHHHHHHHHHHHcCCEEEEccCC--CHHHHHHHHHHHHH--cCCCEEEEccCchhhhHHHHHHHHhCCCeEEEecCCC
Confidence 4455566788888888886652111 01111000000001 136888776532 22222222 334578888887332
Q ss_pred C--------cccccccChHHHHHHH-HHHHHHHhh-cC--CEEEEEEeCCCC-CCcHHHHHHHHHHHHHcCCcE
Q 042576 126 G--------KLFLEEYDNKGMRETR-KRAIEKAMK-EA--RTWGIVLGTLGR-QGNPRILERLQKRMEKKGFDY 186 (313)
Q Consensus 126 ~--------~~~~e~~d~~~~l~~R-~~~I~kak~-~A--~~~GIIvgTLg~-Q~~~~ii~~l~~ll~~~Gkk~ 186 (313)
. .+.....|....-+.= ..+++.... .. +.+|+|.++... .....-.+-.++-++++|.+.
T Consensus 90 ~~~~~~~~~~~~~V~~d~~~~g~~~~~~l~~~~~~~g~~~~~i~~i~~~~~~~~~~~~R~~G~~~~l~~~~~~~ 163 (289)
T cd01540 90 VDADGKPMEDVPHVGMSATKIGEQVGEAIADEMKKRGWDPKEVGALRITYDELDTAKPRTDGALEALKAPGFPE 163 (289)
T ss_pred cccCCCccccceEecCCHHHHHHHHHHHHHHHHHhhcCCCcceEEEEecCCCCcchhhHHHHHHHHHhcCCCCc
Confidence 1 1222223332211110 122222220 22 578988754322 222334556677777777664
No 236
>cd06319 PBP1_ABC_sugar_binding_like_10 Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems. Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily, which consists of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis.
Probab=26.53 E-value=4.5e+02 Score=23.21 Aligned_cols=59 Identities=15% Similarity=0.142 Sum_probs=34.8
Q ss_pred CCEEEEEEeCCCCCCcHHHHHHHHHHHHHcCCcEEEEE-eCCCCHHH--------HhcCcCCccEEEEe
Q 042576 153 ARTWGIVLGTLGRQGNPRILERLQKRMEKKGFDYVVIM-MSEISPAR--------VALFEDSVDAWIQI 212 (313)
Q Consensus 153 A~~~GIIvgTLg~Q~~~~ii~~l~~ll~~~Gkk~y~i~-v~einp~K--------Lanf~~~ID~fV~i 212 (313)
.+++|+|-|..+......-.+-.++-++++|.+...+. .+..+.++ |...+ ++|+++..
T Consensus 125 ~~~i~~i~~~~~~~~~~~r~~gf~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~-~~~ai~~~ 192 (277)
T cd06319 125 DGKVGMVAIPQKRKNGQKRTKGFKEAMKEAGCDLAGIRQQKDFSYQETFDYTNDLLTANP-DIRAIWLQ 192 (277)
T ss_pred CCcEEEEeccCCCccHHHHHHHHHHHHHhcCCceEeeccCCCCCHHHHHHHHHHHHHhCC-CCCEEEEC
Confidence 46899988765544344556667788888887754332 34555332 22334 57776543
No 237
>KOG2892 consensus Porphobilinogen deaminase [Coenzyme transport and metabolism]
Probab=26.44 E-value=3.3e+02 Score=26.54 Aligned_cols=78 Identities=17% Similarity=0.297 Sum_probs=51.5
Q ss_pred CChHHHHHHHHHhCCCCC-eEEEEecc----ccHhHH---------HHHHHHHHhCCCeEEecCCCC----CCCccccCC
Q 042576 21 IDVNRLIDTIKVNYSDPG-KLILAGTI----QFASAI---------RAAKPELEKQGFKVMIPQSKP----LSAGEVLGC 82 (313)
Q Consensus 21 iD~~~~i~~i~~~f~~~~-~i~Lv~ti----Qf~~~l---------~~~~~~L~~~g~~v~ipq~~p----ls~GevLGC 82 (313)
|...|+++.+++.+|+.. .|..++|+ ++.... .++.+.|...+.+++|...|. |.+|=++||
T Consensus 20 IQs~~v~~~Lek~YP~l~f~I~t~~T~GDkIl~k~L~~ig~KsLfTkELE~aL~~~~~divVHSLKDlPT~LP~G~~ig~ 99 (320)
T KOG2892|consen 20 IQSYHVREKLEKKYPELAFEIITMSTTGDKILSKPLAKIGGKSLFTKELEDALINGHVDIVVHSLKDLPTYLPEGMIIGC 99 (320)
T ss_pred hhHHHHHHHHHhhCCCceeEEEEecccchHHhhchHhhhcccchhHHHHHHHHhcCCccEEEEecccccccCCCCcEecc
Confidence 567899999999998754 36555553 222221 234455555566777765543 468999999
Q ss_pred CCCCCCCCCCCCeEEEecC
Q 042576 83 TAPKIPARESDFNLVFIAD 101 (313)
Q Consensus 83 t~~~~~~~~~~d~iv~igd 101 (313)
.-.+.+. .|++||--.
T Consensus 100 i~kRedp---~DalV~~~~ 115 (320)
T KOG2892|consen 100 ILKREDP---RDALVFLTY 115 (320)
T ss_pred ccCCCCc---cceEEEecc
Confidence 8877643 489988643
No 238
>cd03819 GT1_WavL_like This family is most closely related to the GT1 family of glycosyltransferases. WavL in Vibrio cholerae has been shown to be involved in the biosynthesis of the lipopolysaccharide core.
Probab=26.34 E-value=1.6e+02 Score=27.08 Aligned_cols=41 Identities=20% Similarity=0.334 Sum_probs=20.2
Q ss_pred CEEEEEEeCCCCCCcHH-HHHHHHHHHHHcCCcEEEEEeCCCC
Q 042576 154 RTWGIVLGTLGRQGNPR-ILERLQKRMEKKGFDYVVIMMSEIS 195 (313)
Q Consensus 154 ~~~GIIvgTLg~Q~~~~-ii~~l~~ll~~~Gkk~y~i~v~ein 195 (313)
+.+-+.+|.++.+.... +++.++ .|++.+....++++|.-+
T Consensus 185 ~~~i~~~Gr~~~~Kg~~~li~~~~-~l~~~~~~~~l~ivG~~~ 226 (355)
T cd03819 185 KPVILLPGRLTRWKGQEVFIEALA-RLKKDDPDVHLLIVGDAQ 226 (355)
T ss_pred ceEEEEeeccccccCHHHHHHHHH-HHHhcCCCeEEEEEECCc
Confidence 34445556665544443 333333 334445556666666443
No 239
>cd01981 Pchlide_reductase_B Pchlide_reductase_B: B protein of the NB protein complex of Protochlorophyllide (Pchlide)_reductase. Pchlide reductase catalyzes the reductive formation of chlorophyllide (chlide) from protochlorophyllide (pchlide) during biosynthesis of chlorophylls and bacteriochlorophylls. This group contains both the light-independent Pchlide reductase (DPOR) and light-dependent Pchlide reductase (LPOR). Angiosperms contain only LPOR, cyanobacteria, algae and gymnosperms contain both DPOR and LPOR, primitive anoxygenic photosynthetic bacteria contain only DPOR. NB is structurally similar to the FeMo protein of nitrogenase, forming an N2B2 heterotetramer. N and B are homologous to the FeMo alpha and beta subunits respectively. Also in common with nitrogenase in vitro DPOR activity requires ATP hydrolysis and dithoionite or ferredoxin as electron donor. The NB protein complex may serve as a catalytic site for Pchlide reduction similar to MoFe for nitrogen reduction.
Probab=26.32 E-value=1e+02 Score=30.72 Aligned_cols=79 Identities=11% Similarity=0.059 Sum_probs=54.3
Q ss_pred cCCEEEEEEeCCCCCCcHHHHHHHHHHHHHcCCcEEEEEeCCCCHHHHhcCcCCccEEEEecCCCcccccc----CCCCC
Q 042576 152 EARTWGIVLGTLGRQGNPRILERLQKRMEKKGFDYVVIMMSEISPARVALFEDSVDAWIQIACPRLSIDWG----DAFTK 227 (313)
Q Consensus 152 ~A~~~GIIvgTLg~Q~~~~ii~~l~~ll~~~Gkk~y~i~v~einp~KLanf~~~ID~fV~iaCPrlsid~~----~~f~k 227 (313)
..+++-||=.+-..-..+.=++.|+++|++.|.+...++.+.-+.+.|...+ +.++=|. -||+...... +.|-.
T Consensus 161 ~~~~VNiiG~~~~~~~~~~d~~ei~~lL~~~Gl~v~~~~~~~~~~~~i~~~~-~A~lniv-~~~~~~~~~a~~L~~~~Gi 238 (430)
T cd01981 161 EKPSVNLIGPSSLGFHNRHDCRELKRLLHTLGIEVNVVIPEGASVDDLNELP-KAWFNIV-PYREYGLSAALYLEEEFGM 238 (430)
T ss_pred CCCcEEEEcCCCCCCCCcchHHHHHHHHHHcCCeEEEEEcCCCCHHHHHhhh-hCeEEEE-ecHHHHHHHHHHHHHHhCC
Confidence 3456777654432223345566889999999999999999999999999998 4443332 3887655433 56888
Q ss_pred cccCH
Q 042576 228 PLLTP 232 (313)
Q Consensus 228 PvLTP 232 (313)
|.+..
T Consensus 239 P~~~~ 243 (430)
T cd01981 239 PSVKI 243 (430)
T ss_pred CeEec
Confidence 87743
No 240
>TIGR01481 ccpA catabolite control protein A. Catabolite control protein A is a LacI family global transcriptional regulator found in Gram-positive bacteria. CcpA is involved in repressing carbohydrate utilization genes [ex: alpha-amylase (amyE), acetyl-coenzyme A synthase (acsA)] and in activating genes involved in transporting excess carbon from the cell [ex: acetate kinase (ackA), alpha-acetolactate synthase (alsS)]. Additionally, disruption of CcpA in Bacillus megaterium, Staphylococcus xylosus, Lactobacillus casei and Lactocacillus pentosus also decreases growth rate, which suggests CcpA is involved in the regulation of other metabolic pathways.
Probab=26.23 E-value=5.2e+02 Score=23.79 Aligned_cols=139 Identities=16% Similarity=0.155 Sum_probs=67.2
Q ss_pred eEEEEe-c---cccHhHHHHHHHHHHhCCCeEEecCCCC--CCCccccCCCCCCCCCCCCCCeEEEecCCcccHHHHHhh
Q 042576 39 KLILAG-T---IQFASAIRAAKPELEKQGFKVMIPQSKP--LSAGEVLGCTAPKIPARESDFNLVFIADGRFHLEAFMIS 112 (313)
Q Consensus 39 ~i~Lv~-t---iQf~~~l~~~~~~L~~~g~~v~ipq~~p--ls~GevLGCt~~~~~~~~~~d~iv~igdGrFHle~~mi~ 112 (313)
.|+++. + --|...++.+.+.++++|+.+++-.... -..-+.+. .+.. ..+|++|+++...-....-.+.
T Consensus 61 ~Igvv~~~~~~~f~~~l~~~i~~~~~~~g~~~~i~~~~~~~~~~~~~~~----~l~~-~~vdGiIi~~~~~~~~~~~~l~ 135 (329)
T TIGR01481 61 TVGVIIPDISNIYYAELARGIEDIATMYKYNIILSNSDEDPEKEVQVLN----TLLS-KQVDGIIFMGGTITEKLREEFS 135 (329)
T ss_pred EEEEEeCCCCchhHHHHHHHHHHHHHHcCCEEEEEeCCCCHHHHHHHHH----HHHh-CCCCEEEEeCCCCChHHHHHHH
Confidence 477664 2 2355556778888999999977632210 00001110 0001 2378988876421111111233
Q ss_pred CCCceEEEeCCCC--CcccccccChHHHHHHHHHHHHH--HhhcCCEEEEEEeCCCCCCc-HHHHHHHHHHHHHcCCcE
Q 042576 113 NPGIKTFRYDPYL--GKLFLEEYDNKGMRETRKRAIEK--AMKEARTWGIVLGTLGRQGN-PRILERLQKRMEKKGFDY 186 (313)
Q Consensus 113 np~~~~y~yDPys--~~~~~e~~d~~~~l~~R~~~I~k--ak~~A~~~GIIvgTLg~Q~~-~~ii~~l~~ll~~~Gkk~ 186 (313)
...+|++.+|-.. ..+.....|.... -|. +++. .+ .-+++|+|.|....... ..-.+-.++-++++|.+.
T Consensus 136 ~~~iPvV~~~~~~~~~~~~~V~~D~~~~--~~~-a~~~L~~~-G~~~I~~i~g~~~~~~~~~~R~~Gf~~~l~~~g~~~ 210 (329)
T TIGR01481 136 RSPVPVVLAGTVDKENELPSVNIDYKQA--TKE-AVGELIAK-GHKSIAFVGGPLSDSINGEDRLEGYKEALNKAGIQF 210 (329)
T ss_pred hcCCCEEEEecCCCCCCCCEEEECcHHH--HHH-HHHHHHHC-CCCeEEEEecCcccccchHHHHHHHHHHHHHcCCCC
Confidence 3467877776332 1122222332221 111 1222 23 56799999776532221 334455667788888653
No 241
>PF01656 CbiA: CobQ/CobB/MinD/ParA nucleotide binding domain; InterPro: IPR002586 This entry consists of various cobyrinic acid a,c-diamide synthases. These include CbiA and CbiP from Salmonella typhimurium []., and CobQ from Rhodobacter capsulatus []. These amidases catalyse amidations to various side chains of hydrogenobyrinic acid or cobyrinic acid a,c-diamide in the biosynthesis of cobalamin (vitamin B12) from uroporphyrinogen III. Vitamin B12 is an important cofactor and an essential nutrient for many plants and animals and is primarily produced by bacteria [].; PDB: 3K9G_A 3K9H_B 3EZ9_B 3EZF_A 3EZ2_B 3EZ6_A 3EZ7_A 1G3Q_A 1G3R_A 1DTS_A ....
Probab=26.10 E-value=2e+02 Score=24.35 Aligned_cols=41 Identities=22% Similarity=0.333 Sum_probs=34.9
Q ss_pred EEEeCCCCCCcHHHHHHHHHHHHHcCCcEEEEEeCCCCHHH
Q 042576 158 IVLGTLGRQGNPRILERLQKRMEKKGFDYVVIMMSEISPAR 198 (313)
Q Consensus 158 IIvgTLg~Q~~~~ii~~l~~ll~~~Gkk~y~i~v~einp~K 198 (313)
.|+|++||-|--.+.-.|-..|.++|+++.++=++--.+.-
T Consensus 2 ~v~~~kGG~GKTt~a~~la~~la~~g~~VlliD~D~~~~~~ 42 (195)
T PF01656_consen 2 AVTSGKGGVGKTTIAANLAQALARKGKKVLLIDLDPQAPNL 42 (195)
T ss_dssp EEEESSTTSSHHHHHHHHHHHHHHTTS-EEEEEESTTSHHH
T ss_pred EEEcCCCCccHHHHHHHHHhccccccccccccccCcccccH
Confidence 47899999999999999999999999999999887655544
No 242
>PF13407 Peripla_BP_4: Periplasmic binding protein domain; PDB: 3BRS_B 3GBP_A 3GA5_A 1GCG_A 1GCA_A 3H75_A 3D02_A 3L49_B 3EJW_B 3T95_A ....
Probab=25.95 E-value=2.2e+02 Score=25.10 Aligned_cols=43 Identities=7% Similarity=0.295 Sum_probs=24.7
Q ss_pred EEEEEeCCCCCCcHHHHHHHHHHHHHcCCcEEEEEeCCCCHHH
Q 042576 156 WGIVLGTLGRQGNPRILERLQKRMEKKGFDYVVIMMSEISPAR 198 (313)
Q Consensus 156 ~GIIvgTLg~Q~~~~ii~~l~~ll~~~Gkk~y~i~v~einp~K 198 (313)
||+|+.+.+-+....+.+-+++.+++.|.+..++.-+.-++++
T Consensus 1 I~vi~~~~~~~~~~~~~~g~~~~a~~~g~~~~~~~~~~~d~~~ 43 (257)
T PF13407_consen 1 IGVIVPSMDNPFWQQVIKGAKAAAKELGYEVEIVFDAQNDPEE 43 (257)
T ss_dssp EEEEESSSSSHHHHHHHHHHHHHHHHHTCEEEEEEESTTTHHH
T ss_pred cEEEeCCCCCHHHHHHHHHHHHHHHHcCCEEEEeCCCCCCHHH
Confidence 4566666666655556666666666666555554444555444
No 243
>cd06310 PBP1_ABC_sugar_binding_like_2 Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems. Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily, which consists of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis.
Probab=25.88 E-value=4.6e+02 Score=23.13 Aligned_cols=136 Identities=12% Similarity=0.100 Sum_probs=64.4
Q ss_pred cHhHHHHHHHHHHhCCCeEEecCCC-CCCCccccCCCCCCCCCCCCCCeEEEecCCcccH--HHH-HhhCCCceEEEeCC
Q 042576 48 FASAIRAAKPELEKQGFKVMIPQSK-PLSAGEVLGCTAPKIPARESDFNLVFIADGRFHL--EAF-MISNPGIKTFRYDP 123 (313)
Q Consensus 48 f~~~l~~~~~~L~~~g~~v~ipq~~-pls~GevLGCt~~~~~~~~~~d~iv~igdGrFHl--e~~-mi~np~~~~y~yDP 123 (313)
|...+..+.+.+++.|+.+.+-... .-.+.+..-.-..... ..+|++++.+.. .+. ..+ .+....+|++..|-
T Consensus 14 ~~~~~~g~~~~~~~~g~~~~~~~~~~~~~~~~~~~~i~~l~~--~~vdgvii~~~~-~~~~~~~l~~~~~~~ipvV~~~~ 90 (273)
T cd06310 14 WQAVKAGAEAAAKELGVKVTFQGPASETDVAGQVNLLENAIA--RGPDAILLAPTD-AKALVPPLKEAKDAGIPVVLIDS 90 (273)
T ss_pred HHHHHHHHHHHHHHcCCEEEEecCccCCCHHHHHHHHHHHHH--hCCCEEEEcCCC-hhhhHHHHHHHHHCCCCEEEecC
Confidence 5556677888888888887652110 0011000000000001 136887766432 331 111 12334667776653
Q ss_pred CC---CcccccccChHHH-HHHHHHHHHHHhhcCCEEEEEEeCCCCCCcHHHHHHHHHHHHHc-CCcEE
Q 042576 124 YL---GKLFLEEYDNKGM-RETRKRAIEKAMKEARTWGIVLGTLGRQGNPRILERLQKRMEKK-GFDYV 187 (313)
Q Consensus 124 ys---~~~~~e~~d~~~~-l~~R~~~I~kak~~A~~~GIIvgTLg~Q~~~~ii~~l~~ll~~~-Gkk~y 187 (313)
.. ..+.....|..+. ...=..++++.. ..+++++|-|...-.....-.+-.++.++++ |.+..
T Consensus 91 ~~~~~~~~~~v~~d~~~~~~~~~~~l~~~~~-g~~~i~~i~~~~~~~~~~~r~~gf~~a~~~~~~~~~~ 158 (273)
T cd06310 91 GLNSDIAVSFVATDNVAAGKLAAEALAELLG-KKGKVAVISFVPGSSTTDQREEGFLEGLKEYPGIEIV 158 (273)
T ss_pred CCCCCcceEEEeeChHHHHHHHHHHHHHHcC-CCceEEEEeCCCCCccHHHHHHHHHHHHHhCCCcEEE
Confidence 21 1122223343222 111233445544 5678988877665444444455566777777 65543
No 244
>cd00133 PTS_IIB PTS_IIB: subunit IIB of enzyme II (EII) is the central energy-coupling domain of the phosphoenolpyruvate:carbohydrate phosphotransferase system (PTS). In the multienzyme PTS complex, EII is a carbohydrate-specific permease consisting of two cytoplasmic domains (IIA and IIB) and a transmembrane channel IIC domain. The IIB domain fold includes a central four-stranded parallel open twisted beta-sheet flanked by alpha-helices on both sides. The seven major PTS systems with this IIB fold include chitobiose/lichenan, ascorbate, lactose, galactitol, mannitol, fructose, and a sensory system with similarity to the bacterial bgl system. The PTS is found only in bacteria, where it catalyzes the transport and phosphorylation of numerous monosaccharides, disaccharides, polyols, amino sugars, and other sugar derivatives. The four proteins (domains) forming the PTS phosphorylation cascade (EI, HPr, EIIA, and EIIB), can phosphorylate or interact with numerous non-PTS proteins thereby r
Probab=25.65 E-value=2.5e+02 Score=19.95 Aligned_cols=50 Identities=20% Similarity=0.281 Sum_probs=29.7
Q ss_pred EEEeCCCCCCcHHHHHHHHHHHHHcCCcEEEEEeCCCCHHHHhcCcCCccEEEE
Q 042576 158 IVLGTLGRQGNPRILERLQKRMEKKGFDYVVIMMSEISPARVALFEDSVDAWIQ 211 (313)
Q Consensus 158 IIvgTLg~Q~~~~ii~~l~~ll~~~Gkk~y~i~v~einp~KLanf~~~ID~fV~ 211 (313)
++++.-|..-+.-+.++|++.+.+.+.. ..+...++... .... ++|.++-
T Consensus 3 l~vc~~G~~~s~~l~~~l~~~~~~~~~~-~~~~~~~~~~~--~~~~-~~dliit 52 (84)
T cd00133 3 LVVCGSGIGSSSMLAEKLEKAAKELGIE-VKVEAQGLSEV--IDLA-DADLIIS 52 (84)
T ss_pred EEECCCcHhHHHHHHHHHHHHHHHCCCe-EEEEEcccchh--hhcC-CccEEEE
Confidence 4555555455556788999999988875 44444444441 2334 4664443
No 245
>PRK12419 riboflavin synthase subunit beta; Provisional
Probab=25.64 E-value=2e+02 Score=25.46 Aligned_cols=85 Identities=9% Similarity=-0.019 Sum_probs=49.9
Q ss_pred CEEEEEEeCCCCCCcHHHHHHHHHHHHHcCCc---EEEEEeCCCC-----HHHHhcCcCCccEEEEecCCC-cc------
Q 042576 154 RTWGIVLGTLGRQGNPRILERLQKRMEKKGFD---YVVIMMSEIS-----PARVALFEDSVDAWIQIACPR-LS------ 218 (313)
Q Consensus 154 ~~~GIIvgTLg~Q~~~~ii~~l~~ll~~~Gkk---~y~i~v~ein-----p~KLanf~~~ID~fV~iaCPr-ls------ 218 (313)
-+||||++-.-..-.-.+++-..+.|+++|.+ ..++-|---+ ..+|+.=. ++|++|-++|== ..
T Consensus 11 ~riaIV~srfn~~It~~Ll~gA~~~l~~~G~~~~~i~v~~VPGA~EiP~~a~~l~~~~-~yDaiIaLG~VIrGeT~H~e~ 89 (158)
T PRK12419 11 QRIAFIQARWHADIVDQARKGFVAEIAARGGAASQVDIFDVPGAFEIPLHAQTLAKTG-RYAAIVAAALVVDGGIYRHEF 89 (158)
T ss_pred CEEEEEEecCCHHHHHHHHHHHHHHHHHcCCCccceEEEECCcHHHHHHHHHHHHhcC-CCCEEEEEEEEEcCCCchhHH
Confidence 48999997654444444444445678888843 4444443222 24566555 699999999931 11
Q ss_pred ---------ccccCCCCCc----ccCHHHHHHHh
Q 042576 219 ---------IDWGDAFTKP----LLTPFEAEIAL 239 (313)
Q Consensus 219 ---------id~~~~f~kP----vLTPyE~~vAL 239 (313)
.+=+-++.+| ||||-..+-|+
T Consensus 90 V~~~v~~gl~~vsl~~~~PV~fGVLT~~~~eqA~ 123 (158)
T PRK12419 90 VAQAVIDGLMRVQLDTEVPVFSVVLTPHHFHESE 123 (158)
T ss_pred HHHHHHHHHHHHHhccCCCEEEEecCCCcHHHHH
Confidence 1123357788 47777666444
No 246
>PF00205 TPP_enzyme_M: Thiamine pyrophosphate enzyme, central domain; InterPro: IPR012000 A number of enzymes require thiamine pyrophosphate (TPP) (vitamin B1) as a cofactor. It has been shown [] that some of these enzymes are structurally related. This central domain of TPP enzymes contains a 2-fold Rossman fold. ; GO: 0000287 magnesium ion binding, 0030976 thiamine pyrophosphate binding; PDB: 1OZH_C 1OZF_B 1OZG_B 2Q29_B 2Q28_A 2Q27_B 1OVM_B 1PVD_A 1PYD_B 2VK1_C ....
Probab=25.56 E-value=68 Score=26.35 Aligned_cols=68 Identities=25% Similarity=0.204 Sum_probs=45.3
Q ss_pred HHHHHhhcCCEEEEEEeCCCCCCcHHHHHHHHHHHHHcCCcEEEEEeCCC-----------------CHHHHhcCcCCcc
Q 042576 145 AIEKAMKEARTWGIVLGTLGRQGNPRILERLQKRMEKKGFDYVVIMMSEI-----------------SPARVALFEDSVD 207 (313)
Q Consensus 145 ~I~kak~~A~~~GIIvgTLg~Q~~~~ii~~l~~ll~~~Gkk~y~i~v~ei-----------------np~KLanf~~~ID 207 (313)
+.+..+ +|++--||+|...+ +....+.+++++++.|..+++-.+++= +++.-..+. +.|
T Consensus 4 ~~~~L~-~A~rP~il~G~g~~--~~~a~~~l~~lae~~~~Pv~~t~~~kg~i~~~hp~~~G~~g~~~~~~~~~~l~-~aD 79 (137)
T PF00205_consen 4 AADLLS-SAKRPVILAGRGAR--RSGAAEELRELAEKLGIPVATTPMGKGVIPEDHPLFLGYLGLFGSPAANEALE-QAD 79 (137)
T ss_dssp HHHHHH-H-SSEEEEE-HHHH--HTTCHHHHHHHHHHHTSEEEEEGGGTTSSTTTSTTEEEESCGGSCHHHHHHHH-HSS
T ss_pred HHHHHH-hCCCEEEEEcCCcC--hhhHHHHHHHHHHHHCCCEEecCccccccCCCCchhcccCCccCCHHHHHHhc-CCC
Confidence 445556 88899999988644 124556788888889999888776652 344344445 678
Q ss_pred EEEEecCCC
Q 042576 208 AWIQIACPR 216 (313)
Q Consensus 208 ~fV~iaCPr 216 (313)
+.+.++|.-
T Consensus 80 lvl~iG~~~ 88 (137)
T PF00205_consen 80 LVLAIGTRL 88 (137)
T ss_dssp EEEEESSSS
T ss_pred EEEEECCCC
Confidence 888888763
No 247
>cd01544 PBP1_GalR Ligand-binding domain of DNA transcription repressor GalR which is one of two regulatory proteins involved in galactose transport and metabolism. Ligand-binding domain of DNA transcription repressor GalR which is one of two regulatory proteins involved in galactose transport and metabolism. Transcription of the galactose regulon genes is regulated by Gal iso-repressor (GalS) and Gal repressor (GalR) in different ways, but both repressors recognize the same DNA binding site in the absence of D-galactose. GalR is a dimeric protein like GalS and is exclusively involved in the regulation of galactose permease, the low-affinity galactose transporter. GalS is involved in regulating expression of the high-affinity galactose transporter encoded by the mgl operon. GalS and GalR are members of the LacI-GalR family of transcription regulators and both contain the type I periplasmic binding protein-like fold. Hence, they are structurally homologous to the periplasmic sugar bindi
Probab=25.51 E-value=4.8e+02 Score=23.20 Aligned_cols=135 Identities=12% Similarity=0.040 Sum_probs=67.6
Q ss_pred cccHhHHHHHHHHHHhCCCeEEecCCCCCCCccccCCCCCCCCCCCCCCeEEEecCCcccHHHHHhhCCCceEEEeCCCC
Q 042576 46 IQFASAIRAAKPELEKQGFKVMIPQSKPLSAGEVLGCTAPKIPARESDFNLVFIADGRFHLEAFMISNPGIKTFRYDPYL 125 (313)
Q Consensus 46 iQf~~~l~~~~~~L~~~g~~v~ipq~~pls~GevLGCt~~~~~~~~~~d~iv~igdGrFHle~~mi~np~~~~y~yDPys 125 (313)
--|...+..+.+.+++.|+.+.+-... +.. .... ..+|++|+.+........ .+..-.+|++.+|-..
T Consensus 17 ~~~~~~~~gi~~~~~~~g~~~~~~~~~----~~~-----~~~~--~~vdgii~~~~~~~~~~~-~~~~~~~pvV~~~~~~ 84 (270)
T cd01544 17 PYYLSIRLGIEKRAQELGIELTKFFRD----DDL-----LEIL--EDVDGIIAIGKFSQEQLA-KLAKLNPNLVFVDSNP 84 (270)
T ss_pred ccHHHHHHHHHHHHHHcCCEEEEEecc----chh-----HHhc--cCcCEEEEecCCCHHHHH-HHHhhCCCEEEECCCC
Confidence 356666788889999999986652110 000 0111 237888887643211111 1333357888777432
Q ss_pred C--cccccccChHHHHHHHHHHHHHH--hhcCCEEEEEEeCCCCC-----CcHHHHHHHHHHHHHcCCc-EEEEEeCCCC
Q 042576 126 G--KLFLEEYDNKGMRETRKRAIEKA--MKEARTWGIVLGTLGRQ-----GNPRILERLQKRMEKKGFD-YVVIMMSEIS 195 (313)
Q Consensus 126 ~--~~~~e~~d~~~~l~~R~~~I~ka--k~~A~~~GIIvgTLg~Q-----~~~~ii~~l~~ll~~~Gkk-~y~i~v~ein 195 (313)
. .+.....|..+. -+. +++.. + ..+++++|.|..+-. -...-.+-.++.++++|.. ...+..+..+
T Consensus 85 ~~~~~~~v~~D~~~a--~~~-~~~~l~~~-g~~~i~~i~~~~~~~~~~~~~~~~R~~gf~~~~~~~~~~~~~~~~~~~~~ 160 (270)
T cd01544 85 APDGFDSVVPDFEQA--VEK-ALDYLLEL-GHTRIGFIGGEEKTTDGHEYIEDPRETAFREYMKEKGLYDPELIYIGDFT 160 (270)
T ss_pred CCCCCCEEEECHHHH--HHH-HHHHHHHc-CCCcEEEECCCcccccccchhhhHHHHHHHHHHHHcCCCChheEeeCCCC
Confidence 1 122222333322 111 11222 4 678899988765411 1122355567778888832 1123445555
Q ss_pred H
Q 042576 196 P 196 (313)
Q Consensus 196 p 196 (313)
.
T Consensus 161 ~ 161 (270)
T cd01544 161 V 161 (270)
T ss_pred H
Confidence 4
No 248
>cd06318 PBP1_ABC_sugar_binding_like_9 Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems. Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily, which consists of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis.
Probab=25.49 E-value=4.8e+02 Score=23.16 Aligned_cols=134 Identities=10% Similarity=0.084 Sum_probs=61.3
Q ss_pred ccHhHHHHHHHHHHhCCCeEEecCCCCCCCccccCCCCCCCCCCCCCCeEEEecCCccc--HHHHH-hhCCCceEEEeCC
Q 042576 47 QFASAIRAAKPELEKQGFKVMIPQSKPLSAGEVLGCTAPKIPARESDFNLVFIADGRFH--LEAFM-ISNPGIKTFRYDP 123 (313)
Q Consensus 47 Qf~~~l~~~~~~L~~~g~~v~ipq~~pls~GevLGCt~~~~~~~~~~d~iv~igdGrFH--le~~m-i~np~~~~y~yDP 123 (313)
-|...+..+.+.+++.|+++++-....-...|.--... ... ..+|++++.+.. .. ...+. +..-.+|+..+|-
T Consensus 13 ~~~~~~~~i~~~~~~~g~~v~~~~~~~~~~~~~~~i~~-~~~--~~~Dgiii~~~~-~~~~~~~i~~~~~~~iPvV~~~~ 88 (282)
T cd06318 13 FFAALTEAAKAHAKALGYELISTDAQGDLTKQIADVED-LLT--RGVNVLIINPVD-PEGLVPAVAAAKAAGVPVVVVDS 88 (282)
T ss_pred HHHHHHHHHHHHHHHcCCEEEEEcCCCCHHHHHHHHHH-HHH--cCCCEEEEecCC-ccchHHHHHHHHHCCCCEEEecC
Confidence 35556677888888888887652111000000000000 001 136887765422 11 11111 1223678887774
Q ss_pred CC----CcccccccChHHHHHHH-HHHHHHHhhcCCEEEEEEeCCCCCCcHHHHHHHHHHHHHcCC
Q 042576 124 YL----GKLFLEEYDNKGMRETR-KRAIEKAMKEARTWGIVLGTLGRQGNPRILERLQKRMEKKGF 184 (313)
Q Consensus 124 ys----~~~~~e~~d~~~~l~~R-~~~I~kak~~A~~~GIIvgTLg~Q~~~~ii~~l~~ll~~~Gk 184 (313)
.. ..+.....|..+.-+.= ..++++..-..+++++|.|..+......-.+-+++-++++|.
T Consensus 89 ~~~~~~~~~~~v~~d~~~~g~~~~~~l~~~~g~~~~~i~~i~~~~~~~~~~~R~~gf~~~l~~~~~ 154 (282)
T cd06318 89 SINLEAGVVTQVQSSNAKNGNLVGEWVVGELGDKPMKIILLSGDAGNLVGQARRDGFLLGVSEAQL 154 (282)
T ss_pred CCCCCcCeEEEEecCcHHHHHHHHHHHHHHhCCCCceEEEEECCCCCchHhHHHHhHHHHHhhCcc
Confidence 32 12222334443332222 223332220234888888765544333444556777777764
No 249
>cd06301 PBP1_rhizopine_binding_like Periplasmic binding proteins specific to rhizopines. Periplasmic binding proteins specific to rhizopines, which are simple sugar-like compounds produced in the nodules induced by the symbiotic root nodule bacteria, such as Rhizobium and Sinorhizobium. Rhizopine-binding-like proteins from other bacteria are also included. Two inositol based rhizopine compounds are known to date: L-3-O-methly-scyllo-inosamine (3-O-MSI) and scyllo-inosamine. Bacterial strains that can metabolize rhizopine have a greater competitive advantage in nodulation and rhizopine synthesis is regulated by NifA/NtrA regulatory transcription activators which are maximally expressed at the onset of nitrogen fixation in bacteroids. The members of this group belong to the pentose/hexose sugar-binding protein family of the type I periplasmic binding protein superfamily.
Probab=25.48 E-value=1.6e+02 Score=26.07 Aligned_cols=8 Identities=25% Similarity=0.833 Sum_probs=3.5
Q ss_pred cCCcEEEE
Q 042576 182 KGFDYVVI 189 (313)
Q Consensus 182 ~Gkk~y~i 189 (313)
.+....++
T Consensus 55 ~~vdgiii 62 (272)
T cd06301 55 QGVDAIIV 62 (272)
T ss_pred cCCCEEEE
Confidence 34444443
No 250
>cd03801 GT1_YqgM_like This family is most closely related to the GT1 family of glycosyltransferases and named after YqgM in Bacillus licheniformis about which little is known. Glycosyltransferases catalyze the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds. The acceptor molecule can be a lipid, a protein, a heterocyclic compound, or another carbohydrate residue. This group of glycosyltransferases is most closely related to the previously defined glycosyltransferase family 1 (GT1). The members of this family may transfer UDP, ADP, GDP, or CMP linked sugars. The diverse enzymatic activities among members of this family reflect a wide range of biological functions. The protein structure available for this family has the GTB topology, one of the two protein topologies observed for nucleotide-sugar-dependent glycosyltransferases. GTB proteins have distinct N- and C- terminal domains each containing a typical Rossmann fold.
Probab=25.43 E-value=1.3e+02 Score=26.78 Aligned_cols=60 Identities=13% Similarity=0.127 Sum_probs=35.3
Q ss_pred HHHHHHHHHHcCCcEEEEEeCCCCHHHHhcCcCCccEEEEecCCC---ccccccCCCCCcccC
Q 042576 172 LERLQKRMEKKGFDYVVIMMSEISPARVALFEDSVDAWIQIACPR---LSIDWGDAFTKPLLT 231 (313)
Q Consensus 172 i~~l~~ll~~~Gkk~y~i~v~einp~KLanf~~~ID~fV~iaCPr---lsid~~~~f~kPvLT 231 (313)
.+.+++++++.+....+...+.++.+.+..+-...|++|..+..+ +++.+.-.+-+|||+
T Consensus 242 ~~~~~~~~~~~~~~~~v~~~g~~~~~~~~~~~~~~di~i~~~~~~~~~~~~~Ea~~~g~pvI~ 304 (374)
T cd03801 242 REELEALAAELGLGDRVTFLGFVPDEDLPALYAAADVFVLPSLYEGFGLVLLEAMAAGLPVVA 304 (374)
T ss_pred HHHHHHHHHHhCCCcceEEEeccChhhHHHHHHhcCEEEecchhccccchHHHHHHcCCcEEE
Confidence 344555555566666677777777666664432688888766542 223334445566654
No 251
>PRK14733 coaE dephospho-CoA kinase; Provisional
Probab=25.38 E-value=92 Score=28.31 Aligned_cols=50 Identities=12% Similarity=0.194 Sum_probs=33.0
Q ss_pred CcHHHHHHHHHHHHHcCCcEEEEEeCCCCHHHHhcCcCCccEEEEecCCCc
Q 042576 167 GNPRILERLQKRMEKKGFDYVVIMMSEISPARVALFEDSVDAWIQIACPRL 217 (313)
Q Consensus 167 ~~~~ii~~l~~ll~~~Gkk~y~i~v~einp~KLanf~~~ID~fV~iaCPrl 217 (313)
-+|.+.+++++.+++.+.+++++-+-=+++..+.... .+|..|.|.||.-
T Consensus 91 ~HP~V~~~~~~~~~~~~~~~vv~eipLL~E~~~~~~~-~~D~vi~V~a~~e 140 (204)
T PRK14733 91 LHPVINKEIKKQVKESDTVMTIVDIPLLGPYNFRHYD-YLKKVIVIKADLE 140 (204)
T ss_pred hhHHHHHHHHHHHHhcCCCeEEEEechhhhccCchhh-hCCEEEEEECCHH
Confidence 5778888888888876655555555444443322223 4889999999974
No 252
>TIGR02990 ectoine_eutA ectoine utilization protein EutA. Members of this protein family are EutA, a predicted arylmalonate decarboxylase found in a conserved ectoine utilization operon of species that include Sinorhizobium meliloti 1021 (where it is known to be induced by ectoine), Mesorhizobium loti and Silicibacter pomeroyi. It is missing from two other species with the other ectoine transport and utilization genes: Pseudomonas putida and Agrobacterium tumefaciens.
Probab=25.19 E-value=2.8e+02 Score=25.82 Aligned_cols=30 Identities=10% Similarity=0.245 Sum_probs=25.2
Q ss_pred CCeEEEEeccccHhHHHH-HHHHHHhCCCeEEe
Q 042576 37 PGKLILAGTIQFASAIRA-AKPELEKQGFKVMI 68 (313)
Q Consensus 37 ~~~i~Lv~tiQf~~~l~~-~~~~L~~~g~~v~i 68 (313)
-+||+|++. |...+++ +++.|++.|++|+-
T Consensus 120 ~~RIalvTP--Y~~~v~~~~~~~l~~~G~eV~~ 150 (239)
T TIGR02990 120 VRRISLLTP--YTPETSRPMAQYFAVRGFEIVN 150 (239)
T ss_pred CCEEEEECC--CcHHHHHHHHHHHHhCCcEEee
Confidence 478999996 8888766 88899999999864
No 253
>PRK03980 flap endonuclease-1; Provisional
Probab=25.08 E-value=1.7e+02 Score=28.14 Aligned_cols=110 Identities=25% Similarity=0.212 Sum_probs=57.4
Q ss_pred ccHHHHHhhCCCceEEEeCCCCCcccccccChHHHHHHHHHHHHHHhhcCCEEEEEE-----eCCCCCCcHHHHHHHHHH
Q 042576 104 FHLEAFMISNPGIKTFRYDPYLGKLFLEEYDNKGMRETRKRAIEKAMKEARTWGIVL-----GTLGRQGNPRILERLQKR 178 (313)
Q Consensus 104 FHle~~mi~np~~~~y~yDPys~~~~~e~~d~~~~l~~R~~~I~kak~~A~~~GIIv-----gTLg~Q~~~~ii~~l~~l 178 (313)
|+-..-|+.+.-+|+|.||--...+..+.+ .+-..+|..+-++++ .|..=|-.. ......-.+++++.++++
T Consensus 15 ~~r~~~ll~~gi~PvfVFDG~~p~~K~~~~--~~rk~~R~~a~~~~~-~~~~~g~~~~a~k~~~~~~~vt~~~~~~~k~l 91 (292)
T PRK03980 15 FYRTINLLENGIKPVYVFDGKPPELKAEEI--EERREVREEAEEKYE-EAKEEGDLEEARKYAQRSSRLTDEIVEDSKKL 91 (292)
T ss_pred HHHHHHHHHCCCEEEEEECCCCchHHHHHH--HHHHHHHHHhHHHHH-HHHHcCCHHHHHHHHhccccCCHHHHHHHHHH
Confidence 333334566667899999976555544432 233444555555544 322111000 000111245689999999
Q ss_pred HHHcCCcEEEEEeC-CCCHHHHhcCcCCccEE-------EEecCCCc
Q 042576 179 MEKKGFDYVVIMMS-EISPARVALFEDSVDAW-------IQIACPRL 217 (313)
Q Consensus 179 l~~~Gkk~y~i~v~-einp~KLanf~~~ID~f-------V~iaCPrl 217 (313)
|+..|..++.---- |---+.|+.-. .+|+. .+.+||+.
T Consensus 92 L~~~GIp~i~AP~EAEAq~A~L~~~g-~vd~V~S~D~D~l~fg~~~v 137 (292)
T PRK03980 92 LDLMGIPYVQAPSEGEAQAAYMAKKG-DAWAVGSQDYDSLLFGAPRL 137 (292)
T ss_pred HHHCCCCEEecCchHHHHHHHHHHCC-CeEEEecCCcCeeeecCCEE
Confidence 99999986654321 23334444333 23332 24568884
No 254
>COG4152 ABC-type uncharacterized transport system, ATPase component [General function prediction only]
Probab=24.90 E-value=6.5e+02 Score=24.44 Aligned_cols=29 Identities=21% Similarity=0.149 Sum_probs=20.8
Q ss_pred HHcCCcEEEEEeCCCCHHHHhcCcCCccEEE
Q 042576 180 EKKGFDYVVIMMSEISPARVALFEDSVDAWI 210 (313)
Q Consensus 180 ~~~Gkk~y~i~v~einp~KLanf~~~ID~fV 210 (313)
++.||+..++- |+.+.+-|+|.+ .|--+-
T Consensus 219 ~~~Gkk~~~ie-s~~s~eeL~~ip-gi~~~~ 247 (300)
T COG4152 219 RSFGKKRLVIE-SDLSLEELANIP-GILKIT 247 (300)
T ss_pred HhcCCceEEEe-ccCchHHHhcCC-Cceeee
Confidence 34677765555 999999999999 665443
No 255
>cd01983 Fer4_NifH The Fer4_NifH superfamily contains a variety of proteins which share a common ATP-binding domain. Functionally, proteins in this superfamily use the energy from hydrolysis of NTP to transfer electron or ion.
Probab=24.89 E-value=1.7e+02 Score=21.16 Aligned_cols=33 Identities=24% Similarity=0.367 Sum_probs=26.3
Q ss_pred EEEeCCCCCCcHHHHHHHHHHHHHcCCcEEEEE
Q 042576 158 IVLGTLGRQGNPRILERLQKRMEKKGFDYVVIM 190 (313)
Q Consensus 158 IIvgTLg~Q~~~~ii~~l~~ll~~~Gkk~y~i~ 190 (313)
|+++..++-|-..+...|...+++.|++..++-
T Consensus 2 ~~~~g~~G~Gktt~~~~l~~~l~~~g~~v~~~~ 34 (99)
T cd01983 2 IVVTGKGGVGKTTLAANLAAALAKRGKRVLLID 34 (99)
T ss_pred EEEECCCCCCHHHHHHHHHHHHHHCCCeEEEEC
Confidence 445555689999999999999999998876554
No 256
>PRK09267 flavodoxin FldA; Validated
Probab=24.84 E-value=1.7e+02 Score=24.89 Aligned_cols=53 Identities=19% Similarity=0.332 Sum_probs=0.0
Q ss_pred EEEEEEeCCCCCCcHHHHHHHHHHHHHcCCcEEEEEeCCCCHHHHhcCcCCccEEEEecCC
Q 042576 155 TWGIVLGTLGRQGNPRILERLQKRMEKKGFDYVVIMMSEISPARVALFEDSVDAWIQIACP 215 (313)
Q Consensus 155 ~~GIIvgTLg~Q~~~~ii~~l~~ll~~~Gkk~y~i~v~einp~KLanf~~~ID~fV~iaCP 215 (313)
++.|+-+|.. -+...++++|.+.|..+ .+-++-+.+..++.|.+++ . |++++|
T Consensus 3 ki~IiY~S~t-GnT~~vA~~Ia~~l~~~--~~~~~~~~~~~~~~l~~~d--~---vi~g~p 55 (169)
T PRK09267 3 KIGIFFGSDT-GNTEDIAKMIQKKLGKD--VADVVDIAKASKEDFEAYD--L---LILGIP 55 (169)
T ss_pred eEEEEEECCC-ChHHHHHHHHHHHhCCC--ceEEEEhhhCCHhhHhhCC--E---EEEEec
No 257
>TIGR02634 xylF D-xylose ABC transporter, substrate-binding protein. Members of this family are periplasmic (when in Gram-negative bacteria) binding proteins for D-xylose import by a high-affinity ATP-binding cassette (ABC) transporter.
Probab=24.62 E-value=1.6e+02 Score=27.28 Aligned_cols=28 Identities=14% Similarity=0.133 Sum_probs=11.7
Q ss_pred EEEEeCCCCCCcHHHHHHHHHHHHHcCC
Q 042576 157 GIVLGTLGRQGNPRILERLQKRMEKKGF 184 (313)
Q Consensus 157 GIIvgTLg~Q~~~~ii~~l~~ll~~~Gk 184 (313)
|+++.+++-.....+.+-+++.+++.|.
T Consensus 2 g~~~~~~~~~~~~~~~~~i~~~a~~~g~ 29 (302)
T TIGR02634 2 GVSIDDLRLERWQKDRDIFVAAAESLGA 29 (302)
T ss_pred eeecCccchhhHHHHHHHHHHHHHhcCC
Confidence 3444444434444444444444444443
No 258
>TIGR01579 MiaB-like-C MiaB-like tRNA modifying enzyme. This clade is a member of a subfamily (TIGR00089) and spans low GC Gram positive bacteria, alpha and epsilon proteobacteria, Campylobacter, Porphyromonas, Aquifex, Thermotoga, Chlamydia, Treponema and Fusobacterium.
Probab=24.53 E-value=1.9e+02 Score=28.75 Aligned_cols=30 Identities=17% Similarity=0.282 Sum_probs=14.6
Q ss_pred HHcCCcEEEEEeC---CCCHHHHhcCcCCccEEE
Q 042576 180 EKKGFDYVVIMMS---EISPARVALFEDSVDAWI 210 (313)
Q Consensus 180 ~~~Gkk~y~i~v~---einp~KLanf~~~ID~fV 210 (313)
++.+.+..+++.| ...|+.+..++ ++|++|
T Consensus 60 k~~~p~~~vvvgGc~a~~~~ee~~~~~-~vD~vv 92 (414)
T TIGR01579 60 RRQNPTAKIIVTGCYAQSNPKELADLK-DVDLVL 92 (414)
T ss_pred HhhCCCcEEEEECCccccCHHHHhcCC-CCcEEE
Confidence 3344444444433 33555555555 566554
No 259
>PRK14481 dihydroxyacetone kinase subunit DhaK; Provisional
Probab=24.49 E-value=2.1e+02 Score=28.24 Aligned_cols=45 Identities=7% Similarity=0.161 Sum_probs=39.1
Q ss_pred cCCEEEEEEeCCCCCCcHH---HHHHHHHHHHHcCCcEEEEEeCCCCH
Q 042576 152 EARTWGIVLGTLGRQGNPR---ILERLQKRMEKKGFDYVVIMMSEISP 196 (313)
Q Consensus 152 ~A~~~GIIvgTLg~Q~~~~---ii~~l~~ll~~~Gkk~y~i~v~einp 196 (313)
+...+.++|+.||+--.++ +.+++.++|+++|.+.+.+.+|..-.
T Consensus 250 ~gd~v~lLvN~LG~ts~lEl~i~~~~v~~~L~~~gi~i~r~~vG~~~T 297 (331)
T PRK14481 250 AGDEVLVLVNGMGATPLMELYIVYNDVAELLEERGVTVARSLVGNYMT 297 (331)
T ss_pred CCCeEEEEEeCCCCCcHHHHHHHHHHHHHHHHHCCCEEEEEEeecccc
Confidence 5678999999999999988 67888999999999999998887643
No 260
>COG1794 RacX Aspartate racemase [Cell envelope biogenesis, outer membrane]
Probab=24.44 E-value=1.5e+02 Score=27.76 Aligned_cols=34 Identities=29% Similarity=0.497 Sum_probs=27.2
Q ss_pred CCeEEEEeccccHhHHHHHHHHHHhCCCeEEecCC
Q 042576 37 PGKLILAGTIQFASAIRAAKPELEKQGFKVMIPQS 71 (313)
Q Consensus 37 ~~~i~Lv~tiQf~~~l~~~~~~L~~~g~~v~ipq~ 71 (313)
-+|++|++| .|.=...--++.|+++|.++++|..
T Consensus 117 ~kkvgLLgT-~~Tm~~~fY~~~l~~~gievvvPdd 150 (230)
T COG1794 117 AKKVGLLGT-RFTMEQGFYRKRLEEKGIEVVVPDD 150 (230)
T ss_pred CceeEEeec-cchHHhHHHHHHHHHCCceEecCCH
Confidence 468999998 5665556667899999999999864
No 261
>cd02117 NifH_like This family contains the NifH (iron protein) of nitrogenase, L subunit (BchL/ChlL) of the protochlorophyllide reductase and the BchX subunit of the Chlorophyllide reductase. Members of this family use energey from ATP hydrolysis and transfer electrons through a Fe4-S4 cluster to other subunit for reduction of substrate.
Probab=24.44 E-value=1.4e+02 Score=26.39 Aligned_cols=33 Identities=18% Similarity=0.290 Sum_probs=28.0
Q ss_pred EEEEEEeCCCCCCcHHHHHHHHHHHHHcCCcEEEE
Q 042576 155 TWGIVLGTLGRQGNPRILERLQKRMEKKGFDYVVI 189 (313)
Q Consensus 155 ~~GIIvgTLg~Q~~~~ii~~l~~ll~~~Gkk~y~i 189 (313)
+|.|. | +||-|--.+.-+|-..|.+.||++.++
T Consensus 2 ~iav~-g-KGGvGKTt~~~nLA~~la~~G~rvLli 34 (212)
T cd02117 2 QIAIY-G-KGGIGKSTTSQNLSAALAEMGKKVLQV 34 (212)
T ss_pred EEEEE-C-CCcCcHHHHHHHHHHHHHHCCCcEEEE
Confidence 45555 7 999999999999999999999986555
No 262
>PRK11041 DNA-binding transcriptional regulator CytR; Provisional
Probab=24.28 E-value=5.4e+02 Score=23.31 Aligned_cols=141 Identities=11% Similarity=0.046 Sum_probs=65.0
Q ss_pred CeEEEEec-c---ccHhHHHHHHHHHHhCCCeEEecCCC--CCCCccccCCCCCCCCCCCCCCeEEEecCCc-ccHHHHH
Q 042576 38 GKLILAGT-I---QFASAIRAAKPELEKQGFKVMIPQSK--PLSAGEVLGCTAPKIPARESDFNLVFIADGR-FHLEAFM 110 (313)
Q Consensus 38 ~~i~Lv~t-i---Qf~~~l~~~~~~L~~~g~~v~ipq~~--pls~GevLGCt~~~~~~~~~~d~iv~igdGr-FHle~~m 110 (313)
..|+++.. . -|...++.+.+.+++.|+++++.... .....+++- .... ..+|++++.+... +.. ...
T Consensus 36 ~~ig~v~~~~~~~~~~~~~~gi~~~~~~~g~~~~~~~~~~~~~~~~~~i~---~l~~--~~vDgiIi~~~~~~~~~-~~~ 109 (309)
T PRK11041 36 RTILVIVPDICDPFFSEIIRGIEVTAAEHGYLVLIGDCAHQNQQEKTFVN---LIIT--KQIDGMLLLGSRLPFDA-SKE 109 (309)
T ss_pred cEEEEEeCCCcCccHHHHHHHHHHHHHHCCCEEEEEeCCCChHHHHHHHH---HHHH--cCCCEEEEecCCCChHH-HHH
Confidence 35776643 1 24555677888999999987652110 000000000 0001 2479988876421 111 111
Q ss_pred hhCCCceEEEeCCCC--CcccccccChHHHHHHHHHHHHHHhhcCCEEEEEEeCCCCCCcHHHHHHHHHHHHHcCCcE
Q 042576 111 ISNPGIKTFRYDPYL--GKLFLEEYDNKGMRETRKRAIEKAMKEARTWGIVLGTLGRQGNPRILERLQKRMEKKGFDY 186 (313)
Q Consensus 111 i~np~~~~y~yDPys--~~~~~e~~d~~~~l~~R~~~I~kak~~A~~~GIIvgTLg~Q~~~~ii~~l~~ll~~~Gkk~ 186 (313)
......++...|-+. ..+.....|..+. -+..+=.-++..-+++++|.|.........-.+-.++-++++|.+.
T Consensus 110 ~~~~~~pvv~~~~~~~~~~~~~V~~Dn~~~--g~~a~~~l~~~G~~~I~~l~~~~~~~~~~~R~~Gf~~~~~~~~~~~ 185 (309)
T PRK11041 110 EQRNLPPMVMANEFAPELELPTVHIDNLTA--AFEAVNYLHELGHKRIACIAGPEEMPLCHYRLQGYVQALRRCGITV 185 (309)
T ss_pred HHhcCCCEEEEccccCCCCCCEEEECcHHH--HHHHHHHHHHcCCceEEEEeCCccccchHHHHHHHHHHHHHcCCCC
Confidence 221112455544321 1122222332221 1211111112155789999877553333344555677788888753
No 263
>cd03813 GT1_like_3 This family is most closely related to the GT1 family of glycosyltransferases. Glycosyltransferases catalyze the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds. The acceptor molecule can be a lipid, a protein, a heterocyclic compound, or another carbohydrate residue. This group of glycosyltransferases is most closely related to the previously defined glycosyltransferase family 1 (GT1). The members of this family may transfer UDP, ADP, GDP, or CMP linked sugars. The diverse enzymatic activities among members of this family reflect a wide range of biological functions. The protein structure available for this family has the GTB topology, one of the two protein topologies observed for nucleotide-sugar-dependent glycosyltransferases. GTB proteins have distinct N- and C- terminal domains each containing a typical Rossmann fold. The two domains have high structural homology despite minimal sequence homolog
Probab=24.08 E-value=1.8e+02 Score=29.30 Aligned_cols=56 Identities=16% Similarity=0.226 Sum_probs=37.9
Q ss_pred CEEEEEEeCCCCCCcHHHHHHHHHHHHHcCCcEEEEEeCCCCHHHHhcCcCCccEEEEecC
Q 042576 154 RTWGIVLGTLGRQGNPRILERLQKRMEKKGFDYVVIMMSEISPARVALFEDSVDAWIQIAC 214 (313)
Q Consensus 154 ~~~GIIvgTLg~Q~~~~ii~~l~~ll~~~Gkk~y~i~v~einp~KLanf~~~ID~fV~iaC 214 (313)
+.-.+|+|.- .......+.+++++++.|..-.+.++|.-.... -+. ..|++|+.+-
T Consensus 324 ~~~l~IvG~g--~~~~~~~~e~~~li~~l~l~~~V~f~G~~~v~~--~l~-~aDv~vlpS~ 379 (475)
T cd03813 324 DAEGWVIGPT--DEDPEYAEECRELVESLGLEDNVKFTGFQNVKE--YLP-KLDVLVLTSI 379 (475)
T ss_pred CeEEEEECCC--CcChHHHHHHHHHHHHhCCCCeEEEcCCccHHH--HHH-hCCEEEeCch
Confidence 4556777752 245567788888888888877777788433333 345 6899998764
No 264
>cd01473 vWA_CTRP CTRP for CS protein-TRAP-related protein: Adhesion of Plasmodium to host cells is an important phenomenon in parasite invasion and in malaria associated pathology.CTRP encodes a protein containing a putative signal sequence followed by a long extracellular region of 1990 amino acids, a transmembrane domain, and a short cytoplasmic segment. The extracellular region of CTRP contains two separated adhesive domains. The first domain contains six 210-amino acid-long homologous VWA domain repeats. The second domain contains seven repeats of 87-60 amino acids in length, which share similarities with the thrombospondin type 1 domain found in a variety of adhesive molecules. Finally, CTRP also contains consensus motifs found in the superfamily of haematopoietin receptors. The VWA domains in these proteins likely mediate protein-protein interactions.
Probab=23.96 E-value=2.5e+02 Score=24.76 Aligned_cols=51 Identities=14% Similarity=0.259 Sum_probs=38.6
Q ss_pred cCCEEEEEEeCCCCCCcH--HHHHHHHHHHHHcCCcEEEEEeCCCCHHHHhcCc
Q 042576 152 EARTWGIVLGTLGRQGNP--RILERLQKRMEKKGFDYVVIMMSEISPARVALFE 203 (313)
Q Consensus 152 ~A~~~GIIvgTLg~Q~~~--~ii~~l~~ll~~~Gkk~y~i~v~einp~KLanf~ 203 (313)
+++++.||+ |=|..... .-+....+.|+++|.+.|+|-+|..+.+.|..+.
T Consensus 107 ~~~kv~Ill-TDG~s~~~~~~~~~~~a~~lk~~gV~i~~vGiG~~~~~el~~ia 159 (192)
T cd01473 107 DAPKVTMLF-TDGNDTSASKKELQDISLLYKEENVKLLVVGVGAASENKLKLLA 159 (192)
T ss_pred cCCeEEEEE-ecCCCCCcchhhHHHHHHHHHHCCCEEEEEEeccccHHHHHHhc
Confidence 357886666 55555432 3455667788999999999999999999888887
No 265
>cd06323 PBP1_ribose_binding Periplasmic sugar-binding domain of the thermophilic Thermoanaerobacter tengcongensis ribose binding protein (ttRBP) and its mesophilic homologs. Periplasmic sugar-binding domain of the thermophilic Thermoanaerobacter tengcongensis ribose binding protein (ttRBP) and its mesophilic homologs. Members of this group are belonging to the type I periplasmic binding protein superfamily, whose members are involved in chemotaxis, ATP-binding cassette transport, and intercellular communication in central nervous system. The thermophilic and mesophilic ribose-binding proteins are structurally very similar, but differ substantially in thermal stability.
Probab=23.74 E-value=1.2e+02 Score=26.77 Aligned_cols=28 Identities=21% Similarity=0.230 Sum_probs=13.5
Q ss_pred EEEEEeCCCCCCcHHHHHHHHHHHHHcC
Q 042576 156 WGIVLGTLGRQGNPRILERLQKRMEKKG 183 (313)
Q Consensus 156 ~GIIvgTLg~Q~~~~ii~~l~~ll~~~G 183 (313)
||+|+.++.-..+..+++.+++.+++.|
T Consensus 2 I~vv~~~~~~~~~~~~~~~i~~~~~~~g 29 (268)
T cd06323 2 IGLSVSTLNNPFFVTLKDGAQKEAKELG 29 (268)
T ss_pred eeEecccccCHHHHHHHHHHHHHHHHcC
Confidence 4445544444444445555555555544
No 266
>TIGR02014 BchZ chlorophyllide reductase subunit Z. This model represents the Z subunit of the three-subunit enzyme, (bacterio)chlorophyllide reductase. This enzyme is responsible for the reduction of the chlorin B-ring and is closely related to the protochlorophyllide reductase complex which reduces the D-ring. Both of these complexes in turn are homologous to nitrogenase.
Probab=23.68 E-value=1.4e+02 Score=30.65 Aligned_cols=77 Identities=18% Similarity=0.201 Sum_probs=57.1
Q ss_pred cCCEEEEEEeCCCCCCcHHHHHHHHHHHHHcCCcEEEEEeCCCCHHHHhcCcCCccEEEEecCCCccccccCCCCCccc
Q 042576 152 EARTWGIVLGTLGRQGNPRILERLQKRMEKKGFDYVVIMMSEISPARVALFEDSVDAWIQIACPRLSIDWGDAFTKPLL 230 (313)
Q Consensus 152 ~A~~~GIIvgTLg~Q~~~~ii~~l~~ll~~~Gkk~y~i~v~einp~KLanf~~~ID~fV~iaCPrlsid~~~~f~kPvL 230 (313)
..+++-||=.+-+.-.++.=++.|+++|+.-|.++..+.-..-+.+.|.+.+ +-++=|.+ |++.+---.+.|-.|.+
T Consensus 151 ~~~~VNIiG~~~g~~~~~~Dl~ElkrlL~~~Gi~vn~v~~~Gtsv~di~~l~-~A~~nIv~-~~~~a~~L~e~~GvP~l 227 (468)
T TIGR02014 151 AKPRVNIIGPTYGCFNMPSDLAEIRRLVEGIGAEVAHVYPLGSHLAEITKLK-NADANIVM-YREFGRGLAEKLGKPYL 227 (468)
T ss_pred CCCeEEEECCCcCcCCChhHHHHHHHHHHHcCCcEEEEcCCcCCHHHHHhhc-cCcEEEee-cHHHHHHHHHHHCCCcc
Confidence 3456877765555555677778899999999999999999999999999998 55555555 77754444446777754
No 267
>cd01539 PBP1_GGBP Periplasmic glucose/galactose-binding protein (GGBP) involved in chemotaxis towards, and active transport of, glucose and galactose in various bacterial species. Periplasmic glucose/galactose-binding protein (GGBP) involved in chemotaxis towards, and active transport of, glucose and galactose in various bacterial species. GGBP is a member of the pentose/hexose sugar-binding protein family of the type I periplasmic binding protein superfamily which consists of two alpha/beta globular domains connected by a three-stranded hinge. This Venus flytrap-like domain undergoes transition from an open to a closed conformational state upon ligand binding. Moreover, the periplasmic GGBP is homologous to the ligand-binding domain of eukaryotic receptors such as glutamate receptor (GluR) and DNA-binding transcriptional repressors such as LacI and GalR.
Probab=23.60 E-value=1.5e+02 Score=27.40 Aligned_cols=26 Identities=12% Similarity=0.101 Sum_probs=14.7
Q ss_pred EEEEEeCCCCCCcHHHHHHHHHHHHH
Q 042576 156 WGIVLGTLGRQGNPRILERLQKRMEK 181 (313)
Q Consensus 156 ~GIIvgTLg~Q~~~~ii~~l~~ll~~ 181 (313)
||+|+..+.-.....+++.|++.+++
T Consensus 2 Igviv~~~~~~~~~~~~~gi~~~a~~ 27 (303)
T cd01539 2 IGVFLYKFDDTFISLVRKNLEDIQKE 27 (303)
T ss_pred eEEEeeCCCChHHHHHHHHHHHHHHh
Confidence 55666555544455555556666665
No 268
>cd05566 PTS_IIB_galactitol PTS_IIB_galactitol: subunit IIB of enzyme II (EII) of the galactitol-specific phosphoenolpyruvate:carbohydrate phosphotransferase system (PTS). In this system, EII is a galactitol-specific permease with two cytoplasmic domains (IIA and IIB) and a transmembrane channel IIC domain that are expressed on three distinct polypeptide chains, in contrast to other PTS sugar transporters. The three genes encoding these subunits (gatA, gatB, and gatC) comprise the gatCBA operon. Galactitol PTS permease takes up exogenous galactitol, releasing the phosphate ester into the cytoplasm in preparation for oxidation and further metabolism via a modified glycolytic pathway called the tagatose-6-phosphate glycolytic pathway. The IIB domain fold includes a central four-stranded parallel open twisted beta-sheet flanked by alpha-helices on both sides. The seven major PTS systems with this IIB fold include galactitol, chitobiose/lichenan, ascorbate, lactose, mannitol, fructose, and
Probab=23.43 E-value=2.2e+02 Score=21.46 Aligned_cols=54 Identities=15% Similarity=0.205 Sum_probs=31.6
Q ss_pred EEEeCCCCCCcHHHHHHHHHHHHHcCCcEEEEEeCCCCHHHHhcCcCCccEEEEecCC
Q 042576 158 IVLGTLGRQGNPRILERLQKRMEKKGFDYVVIMMSEISPARVALFEDSVDAWIQIACP 215 (313)
Q Consensus 158 IIvgTLg~Q~~~~ii~~l~~ll~~~Gkk~y~i~v~einp~KLanf~~~ID~fV~iaCP 215 (313)
++++.-|..-+.-+..+|++.+.+.+....+-.++....+. ... ++| +|+++.|
T Consensus 4 livC~~G~~tS~~l~~~i~~~~~~~~i~~~v~~~~~~~~~~--~~~-~~D-liist~~ 57 (89)
T cd05566 4 LVACGTGVATSTVVASKVKELLKENGIDVKVEQCKIAEVPS--LLD-DAD-LIVSTTK 57 (89)
T ss_pred EEECCCCccHHHHHHHHHHHHHHHCCCceEEEEecHHHhhc--ccC-CCc-EEEEcCC
Confidence 44555554445578899999999888865554334332222 234 588 4444444
No 269
>PF09314 DUF1972: Domain of unknown function (DUF1972); InterPro: IPR015393 This domain is functionally uncharacterised and found in bacterial glycosyltransferases and rhamnosyltransferases.
Probab=23.23 E-value=1.4e+02 Score=26.94 Aligned_cols=58 Identities=24% Similarity=0.332 Sum_probs=45.4
Q ss_pred EEEeCCCCCC----cHHHHHHHHHHHHHcCCcEEEEEeCCCCHHHHhcCcCCccEEEEecCCCc
Q 042576 158 IVLGTLGRQG----NPRILERLQKRMEKKGFDYVVIMMSEISPARVALFEDSVDAWIQIACPRL 217 (313)
Q Consensus 158 IIvgTLg~Q~----~~~ii~~l~~ll~~~Gkk~y~i~v~einp~KLanf~~~ID~fV~iaCPrl 217 (313)
-|+||.|.-. .-..+++|-..|.++|.++++.-.++-.+.+...+. .++++.+ .-|++
T Consensus 5 aIiGtrGIPa~YGGfET~ve~L~~~l~~~g~~v~Vyc~~~~~~~~~~~y~-gv~l~~i-~~~~~ 66 (185)
T PF09314_consen 5 AIIGTRGIPARYGGFETFVEELAPRLVSKGIDVTVYCRSDYYPYKEFEYN-GVRLVYI-PAPKN 66 (185)
T ss_pred EEEeCCCCCcccCcHHHHHHHHHHHHhcCCceEEEEEccCCCCCCCcccC-CeEEEEe-CCCCC
Confidence 4789998744 446889999999999999998888887777777777 6888774 55654
No 270
>cd06275 PBP1_PurR Ligand-binding domain of purine repressor, PurR, which functions as the master regulatory protein of de novo purine nucleotide biosynthesis in Escherichia coli. Ligand-binding domain of purine repressor, PurR, which functions as the master regulatory protein of de novo purine nucleotide biosynthesis in Escherichia coli. This dimeric PurR belongs to the LacI-GalR family of transcription regulators and is activated to bind to DNA operator sites by initially binding either of high affinity corepressors, hypoxanthine or guanine. PurR is composed of two functional domains: aan N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the purine transcription repressor undergoes a
Probab=23.05 E-value=5.2e+02 Score=22.69 Aligned_cols=128 Identities=14% Similarity=0.170 Sum_probs=61.1
Q ss_pred cHhHHHHHHHHHHhCCCeEEecCC--CCCCCccccCCCCCCCCCCCCCCeEEEecCCcccHHH--HHhhCCCceEEEeCC
Q 042576 48 FASAIRAAKPELEKQGFKVMIPQS--KPLSAGEVLGCTAPKIPARESDFNLVFIADGRFHLEA--FMISNPGIKTFRYDP 123 (313)
Q Consensus 48 f~~~l~~~~~~L~~~g~~v~ipq~--~pls~GevLGCt~~~~~~~~~~d~iv~igdGrFHle~--~mi~np~~~~y~yDP 123 (313)
|...++.+.+.+++.|+++++-.. .+-..-+.+. .+.. ..+|++++.+... .... .......+|++.+|-
T Consensus 14 ~~~~~~gi~~~~~~~g~~~~~~~~~~~~~~~~~~i~----~l~~-~~vdgiii~~~~~-~~~~~~~l~~~~~ipvV~i~~ 87 (269)
T cd06275 14 FAEVVRGVEQYCYRQGYNLILCNTEGDPERQRSYLR----MLAQ-KRVDGLLVMCSEY-DQPLLAMLERYRHIPMVVMDW 87 (269)
T ss_pred HHHHHHHHHHHHHHcCCEEEEEeCCCChHHHHHHHH----HHHH-cCCCEEEEecCCC-ChHHHHHHHhcCCCCEEEEec
Confidence 444566777888888888654211 1100000000 0000 1368887765321 1111 111223677777764
Q ss_pred CCC--cccccccChH---HHHHHHHHHHHHHhhcCCEEEEEEeCCCCCCcHHHHHHHHHHHHHcCCcE
Q 042576 124 YLG--KLFLEEYDNK---GMRETRKRAIEKAMKEARTWGIVLGTLGRQGNPRILERLQKRMEKKGFDY 186 (313)
Q Consensus 124 ys~--~~~~e~~d~~---~~l~~R~~~I~kak~~A~~~GIIvgTLg~Q~~~~ii~~l~~ll~~~Gkk~ 186 (313)
... .+.....|.. ++.... ++ .+ ..+++++|.|..+......-.+-.++.++++|.+.
T Consensus 88 ~~~~~~~~~V~~d~~~~~~~~~~~--l~--~~-G~~~i~~i~~~~~~~~~~~r~~gf~~~~~~~~~~~ 150 (269)
T cd06275 88 GPEDDFADKIQDNSEEGGYLATRH--LI--EL-GHRRIGCITGPLEKAPAQQRLAGFRRAMAEAGLPV 150 (269)
T ss_pred ccCCCCCCeEeeCcHHHHHHHHHH--HH--HC-CCceEEEEeCCCCCccHHHHHHHHHHHHHHcCCCC
Confidence 321 1211223322 222111 11 23 56789999877655444445566677788877653
No 271
>PRK14483 DhaKLM operon coactivator DhaQ; Provisional
Probab=23.04 E-value=2.3e+02 Score=27.91 Aligned_cols=45 Identities=9% Similarity=0.265 Sum_probs=39.0
Q ss_pred cCCEEEEEEeCCCCCCcHH---HHHHHHHHHHHcCCcEEEEEeCCCCH
Q 042576 152 EARTWGIVLGTLGRQGNPR---ILERLQKRMEKKGFDYVVIMMSEISP 196 (313)
Q Consensus 152 ~A~~~GIIvgTLg~Q~~~~---ii~~l~~ll~~~Gkk~y~i~v~einp 196 (313)
+...+.++|+.||+--.++ +.+.+.++|+++|.+.+.+.+|..-.
T Consensus 250 ~gd~v~vlVN~LG~ts~~El~i~~~~v~~~L~~~gi~v~r~~vG~~~T 297 (329)
T PRK14483 250 KGDNFILLINGLGATTLMEQYIFANDIRRLLELEGLQITFVKVGTLLT 297 (329)
T ss_pred CCCeEEEEEeCCCCCcHHHHHHHHHHHHHHHHHCCCEEEEeEeecccC
Confidence 5678999999999999887 57889999999999999999887643
No 272
>PF06414 Zeta_toxin: Zeta toxin; InterPro: IPR010488 This entry represents a domain originally identified in bacterial zeta toxin proteins, where it comprises the whole protein []. It has subsequently been found in a number of other proteins, such as polynucleotide kinase and 2',3'-cyclic-nucleotide 3'-phosphodiesterase. It appears to function as a kinase domain [, ].; GO: 0005524 ATP binding, 0016301 kinase activity; PDB: 2P5T_H 1GVN_B 3Q8X_D.
Probab=22.85 E-value=2.6e+02 Score=24.47 Aligned_cols=50 Identities=24% Similarity=0.313 Sum_probs=31.6
Q ss_pred HHHHHHHHHHHhhcCCEEEEEEeCCCCCCcHHHHHHHHHHHHHcCCcEEEEEeC
Q 042576 139 RETRKRAIEKAMKEARTWGIVLGTLGRQGNPRILERLQKRMEKKGFDYVVIMMS 192 (313)
Q Consensus 139 l~~R~~~I~kak~~A~~~GIIvgTLg~Q~~~~ii~~l~~ll~~~Gkk~y~i~v~ 192 (313)
.+....++++|. +.+.==|+=||++.. ..+.++.+.++++|.++.+++|.
T Consensus 79 ~~~~~~~~~~a~-~~~~nii~E~tl~~~---~~~~~~~~~~k~~GY~v~l~~v~ 128 (199)
T PF06414_consen 79 SRLAEKLIEYAI-ENRYNIIFEGTLSNP---SKLRKLIREAKAAGYKVELYYVA 128 (199)
T ss_dssp HHHHHHHHHHHH-HCT--EEEE--TTSS---HHHHHHHHHHHCTT-EEEEEEE-
T ss_pred HHHHHHHHHHHH-HcCCCEEEecCCCCh---hHHHHHHHHHHcCCceEEEEEEE
Confidence 344566788888 666555778888644 55556778888899998888887
No 273
>PF13614 AAA_31: AAA domain; PDB: 2VED_B 2PH1_A 3EA0_B 3FKQ_A 3KB1_B 1ION_A 3LA6_H 3BFV_B 3CIO_D.
Probab=22.72 E-value=3.2e+02 Score=22.28 Aligned_cols=46 Identities=22% Similarity=0.299 Sum_probs=34.9
Q ss_pred EEEeCCCCCCcHHHHHHHHHHHHHcCCcEEEEEeCCCCHHHHhcCc
Q 042576 158 IVLGTLGRQGNPRILERLQKRMEKKGFDYVVIMMSEISPARVALFE 203 (313)
Q Consensus 158 IIvgTLg~Q~~~~ii~~l~~ll~~~Gkk~y~i~v~einp~KLanf~ 203 (313)
-|+|+.|+.|...++-.|-..|.+.|+++.++=+..-++.-...+.
T Consensus 4 ~v~s~~~g~G~t~~a~~lA~~la~~~~~Vllid~~~~~~~~~~~~~ 49 (157)
T PF13614_consen 4 AVWSPKGGVGKTTLALNLAAALARKGKKVLLIDFDFFSPSLSRLLG 49 (157)
T ss_dssp EEEESSTTSSHHHHHHHHHHHHHHTTT-EEEEE--SSS-HHHHHTT
T ss_pred EEECCCCCCCHHHHHHHHHHHHHhcCCCeEEEECCCCCCCcccccc
Confidence 5789999999999999999999999999777777777775444443
No 274
>KOG1184 consensus Thiamine pyrophosphate-requiring enzyme [Amino acid transport and metabolism; Coenzyme transport and metabolism]
Probab=22.56 E-value=1.1e+02 Score=32.03 Aligned_cols=86 Identities=21% Similarity=0.215 Sum_probs=43.0
Q ss_pred CCeEEEecCCcccHH----HHHhhCCCceEEEeCCCCCccccccc----ChHHHHHHHHHHHHHHhhcCC---EEEEEEe
Q 042576 93 DFNLVFIADGRFHLE----AFMISNPGIKTFRYDPYLGKLFLEEY----DNKGMRETRKRAIEKAMKEAR---TWGIVLG 161 (313)
Q Consensus 93 ~d~iv~igdGrFHle----~~mi~np~~~~y~yDPys~~~~~e~~----d~~~~l~~R~~~I~kak~~A~---~~GIIvg 161 (313)
...|+|+|||.|++. +-||.+ +++.+.+=-..+..|.|.. ..+++.---|.++..|- .++ .++.=+.
T Consensus 434 ~rvilfiGDGs~qlTvQeiStmir~-gl~~~if~~NN~GYTIE~~IH~~~Yn~I~~Wd~~~l~~af-g~~~gk~~~~~v~ 511 (561)
T KOG1184|consen 434 KRVILFIGDGSFQLTVQEISTMIRW-GLKPIIFLINNGGYTIEVEIHDGPYNDIQNWDYTALLEAF-GAGEGKYETHKVR 511 (561)
T ss_pred ceEEEEecCccceeeHHHHHHHHhc-CCCcEEEEEeCCceEEEEeecCCCccccccchHHHHHHhh-cCccceeEEeeec
Confidence 468999999999964 567776 4443333222222222211 12223333455666665 432 3444333
Q ss_pred CCCCCCcHHHHHHHHHHHHHcCCc
Q 042576 162 TLGRQGNPRILERLQKRMEKKGFD 185 (313)
Q Consensus 162 TLg~Q~~~~ii~~l~~ll~~~Gkk 185 (313)
| -.+.++.++..+.++..+
T Consensus 512 ~-----~~e~~~~~~~~~~~~~~~ 530 (561)
T KOG1184|consen 512 T-----EEELVEAIKDATFEKNDK 530 (561)
T ss_pred c-----chHHHHHHhhhhhcccCc
Confidence 3 234555566655444433
No 275
>PF06564 YhjQ: YhjQ protein; InterPro: IPR017746 The YhjQ protein is encoded immediately upstream of bacterial cellulose synthase (bcs) genes in a broad range of bacteria, including both copies of the bcs locus in Klebsiella pneumoniae, and in several species is clearly part of the bcs operon. It is identified as a probable component of the bacterial cellulose metabolic process not only by gene location, but also by partial phylogenetic profiling, or Haft-Selengut algorithm [], based on a bacterial cellulose biosynthesis genome property profile. Cellulose plays an important role in biofilm formation and structural integrity in some bacteria. Mutants in yhjQ in Escherichia coli, show altered morphology an growth, but the function of YhjQ has not yet been determined.
Probab=22.55 E-value=1.6e+02 Score=27.68 Aligned_cols=41 Identities=15% Similarity=0.253 Sum_probs=34.5
Q ss_pred EEEEeCCCCCCcHHHHHHHHHHHHHcCCcEEEEEeCCCCHHHHh
Q 042576 157 GIVLGTLGRQGNPRILERLQKRMEKKGFDYVVIMMSEISPARVA 200 (313)
Q Consensus 157 GIIvgTLg~Q~~~~ii~~l~~ll~~~Gkk~y~i~v~einp~KLa 200 (313)
=.|+|.+||-|...+.-.|-..|.+.|+++..|=+ .|+-+-
T Consensus 4 iai~s~kGGvG~TTltAnLA~aL~~~G~~VlaID~---dpqN~L 44 (243)
T PF06564_consen 4 IAIVSPKGGVGKTTLTANLAWALARLGESVLAIDL---DPQNLL 44 (243)
T ss_pred EEEecCCCCCCHHHHHHHHHHHHHHCCCcEEEEeC---CcHHHH
Confidence 36899999999999999999999999999776655 455555
No 276
>TIGR00550 nadA quinolinate synthetase complex, A subunit. This protein, termed NadA, plays a role in the synthesis of pyridine, a precursor to NAD. The quinolinate synthetase complex consists of A protein (this protein) and B protein. B protein converts L-aspartate to iminoaspartate, an unstable reaction product which in the absence of A protein is spontaneously hydrolyzed to form oxaloacetate. The A protein, NadA, converts iminoaspartate to quinolate.
Probab=22.51 E-value=2e+02 Score=27.95 Aligned_cols=49 Identities=18% Similarity=0.120 Sum_probs=32.6
Q ss_pred CCeEEEecCCcccHHHHHhhCCCceEEEeCCCCCcccccccChHHHHHHH
Q 042576 93 DFNLVFIADGRFHLEAFMISNPGIKTFRYDPYLGKLFLEEYDNKGMRETR 142 (313)
Q Consensus 93 ~d~iv~igdGrFHle~~mi~np~~~~y~yDPys~~~~~e~~d~~~~l~~R 142 (313)
.+.|||.|+ +|-.|.+.+-+|++.++.=|+..+=...+..+.+.+++.|
T Consensus 53 ~~~IvF~gv-~fMae~a~~l~p~k~vilp~~~a~C~~a~~~~~~~i~~lk 101 (310)
T TIGR00550 53 ADIIVFCGV-HFMGETAKILNPEKTVLMPDLGAGCSMADMCPPEEFKKLK 101 (310)
T ss_pred CCEEEEeCC-chHHHHHHHhCCCCEEEccCCCCCCccccccCHHHHHHHH
Confidence 578999998 6888999998899988875554443333334444444333
No 277
>cd06292 PBP1_LacI_like_10 Ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. This group includes the ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.
Probab=22.48 E-value=5.4e+02 Score=22.69 Aligned_cols=130 Identities=18% Similarity=0.227 Sum_probs=62.2
Q ss_pred ccHhHHHHHHHHHHhCCCeEEecCC--CCCCCccccCCCCCCCCCCCCCCeEEEecCC--ccc-----HHHHHhhCCCce
Q 042576 47 QFASAIRAAKPELEKQGFKVMIPQS--KPLSAGEVLGCTAPKIPARESDFNLVFIADG--RFH-----LEAFMISNPGIK 117 (313)
Q Consensus 47 Qf~~~l~~~~~~L~~~g~~v~ipq~--~pls~GevLGCt~~~~~~~~~~d~iv~igdG--rFH-----le~~mi~np~~~ 117 (313)
-|...++.+.+.+++.|+++++-.. .+-..-+.+. .+.. ..+|++++.+.. .-+ +.. +...+.|
T Consensus 13 ~~~~~~~gi~~~~~~~g~~~~~~~~~~~~~~~~~~i~----~l~~-~~vdgiIi~~~~~~~~~~~~~~i~~--~~~~~ip 85 (273)
T cd06292 13 IFPAFAEAIEAALAQYGYTVLLCNTYRGGVSEADYVE----DLLA-RGVRGVVFISSLHADTHADHSHYER--LAERGLP 85 (273)
T ss_pred hHHHHHHHHHHHHHHCCCEEEEEeCCCChHHHHHHHH----HHHH-cCCCEEEEeCCCCCcccchhHHHHH--HHhCCCC
Confidence 3455567788888888888654211 1100000000 0000 136887776521 111 111 2334678
Q ss_pred EEEeCCCC---CcccccccChHHHHHHHHHHHHHHhhcCCEEEEEEeCCCCCCcHHHHHHHHHHHHHcCCc
Q 042576 118 TFRYDPYL---GKLFLEEYDNKGMRETRKRAIEKAMKEARTWGIVLGTLGRQGNPRILERLQKRMEKKGFD 185 (313)
Q Consensus 118 ~y~yDPys---~~~~~e~~d~~~~l~~R~~~I~kak~~A~~~GIIvgTLg~Q~~~~ii~~l~~ll~~~Gkk 185 (313)
++.+|-.. ..+.....|..+.-+.=-..+. .+ .-+++++|.|...-.....-.+-.++.++++|.+
T Consensus 86 vV~i~~~~~~~~~~~~V~~d~~~~~~~~~~~l~-~~-g~~~i~~i~~~~~~~~~~~R~~gf~~~~~~~~~~ 154 (273)
T cd06292 86 VVLVNGRAPPPLKVPHVSTDDALAMRLAVRHLV-AL-GHRRIGFASGPGRTVPRRRKIAGFRAALEEAGLE 154 (273)
T ss_pred EEEEcCCCCCCCCCCEEEECcHHHHHHHHHHHH-HC-CCceEEEEeCCcccccHHHHHHHHHHHHHHcCCC
Confidence 88887432 1222223333322211111111 13 5678998887654333344456677778888854
No 278
>cd06306 PBP1_TorT-like TorT-like proteins, a periplasmic binding protein family that activates induction of the Tor respiratory system upon trimethylamine N-oxide (TMAO) electron-acceptor binding in bacteria. TorT-like proteins, a periplasmic binding protein family that activates induction of the Tor respiratory system upon trimethylamine N-oxide (TMAO) electron-acceptor binding in bacteria. The Tor respiratory system is consists of three proteins (TorC, TorA, and TorD) and is induced in the presence of TMAO. The TMAO control is tightly regulated by three proteins: TorS, TorT, and TorR. Thus, the disruption of any of these proteins can abolish the Tor respiratory induction. TorT shares homology with the sugar-binding domain of the type I periplasmic binding proteins. The members of TorT-like family bind TMAO or related compounds and are predicted to be involved in signal transduction and/or substrate transport.
Probab=22.45 E-value=5.6e+02 Score=22.85 Aligned_cols=158 Identities=8% Similarity=-0.021 Sum_probs=77.6
Q ss_pred ccHhHHHHHHHHHHhCCCeEEecCCC--CCCCccccCCCCCCCCCCCCCCeEEEecCCcccHH-HHHhhCCCceEEEeCC
Q 042576 47 QFASAIRAAKPELEKQGFKVMIPQSK--PLSAGEVLGCTAPKIPARESDFNLVFIADGRFHLE-AFMISNPGIKTFRYDP 123 (313)
Q Consensus 47 Qf~~~l~~~~~~L~~~g~~v~ipq~~--pls~GevLGCt~~~~~~~~~~d~iv~igdGrFHle-~~mi~np~~~~y~yDP 123 (313)
-|...+..+.+.+++.|+++++-... +-...|+ .--...+. ..+|++++.+...-... -..+....+|++.+|-
T Consensus 13 f~~~~~~gi~~~a~~~g~~~~~~~~~~~~~~~~~~-~~i~~~~~--~~vdgiI~~~~~~~~~~~~~~~~~~giPvV~~~~ 89 (268)
T cd06306 13 YWLSVNYGMVEEAKRLGVSLKLLEAGGYPNLAKQI-AQLEDCAA--WGADAILLGAVSPDGLNEILQQVAASIPVIALVN 89 (268)
T ss_pred HHHHHHHHHHHHHHHcCCEEEEecCCCCCCHHHHH-HHHHHHHH--cCCCEEEEcCCChhhHHHHHHHHHCCCCEEEecc
Confidence 34555667888888889987652110 0000000 00000001 24788887753211111 1122345778887763
Q ss_pred C---CCcccccccC---hHHHHHHHHHHHHHHh--hcCCEEEEEEeCCCCCCcHHHHHHHHHHHHHcCCcEEEEEeCCCC
Q 042576 124 Y---LGKLFLEEYD---NKGMRETRKRAIEKAM--KEARTWGIVLGTLGRQGNPRILERLQKRMEKKGFDYVVIMMSEIS 195 (313)
Q Consensus 124 y---s~~~~~e~~d---~~~~l~~R~~~I~kak--~~A~~~GIIvgTLg~Q~~~~ii~~l~~ll~~~Gkk~y~i~v~ein 195 (313)
. .........| ..+.+. ..++++.. ...+++++|.|..+.+....-.+-+++.++++|.+...+..+.-+
T Consensus 90 ~~~~~~~~~~V~~d~~~~g~~~~--~~l~~~g~~~~~~~~i~~l~g~~~~~~~~~R~~g~~~~~~~~~~~~~~~~~~~~~ 167 (268)
T cd06306 90 DINSPDITAKVGVSWYEMGYQAG--EYLAQRHPKGSKPAKVAWFPGPKGAGWVKAVEKGFRDALAGSAIEISAIKYGDTG 167 (268)
T ss_pred CCCCcceeEEecCChHHHHHHHH--HHHHHHhhcCCCCceEEEEeCCCCCchHHHHHHHHHHHHhhcCcEEeeeccCCcc
Confidence 2 1111112223 222222 22333332 023799999988776655566667778888888776544333334
Q ss_pred HHH--------HhcCcCCccEEE
Q 042576 196 PAR--------VALFEDSVDAWI 210 (313)
Q Consensus 196 p~K--------Lanf~~~ID~fV 210 (313)
.++ |...+ ++|+++
T Consensus 168 ~~~~~~~~~~~l~~~~-~~~~i~ 189 (268)
T cd06306 168 KEVQRKLVEEALEAHP-DIDYIV 189 (268)
T ss_pred HHHHHHHHHHHHHhCC-CcCEEe
Confidence 322 33334 588776
No 279
>cd01973 Nitrogenase_VFe_beta_like Nitrogenase_VFe_beta -like: Nitrogenase VFe protein, beta subunit like. This group contains proteins similar to the beta subunits of the VFe protein of the vanadium-dependent (V-) nitrogenase. Nitrogenase catalyzes the ATP-dependent reduction of dinitrogen (N2) to ammonia. In addition to V-nitrogenase there is a molybdenum (Mo)-dependent nitrogenase and an iron only (Fe-) nitrogenase. The Mo-nitrogenase is the most widespread and best characterized of these systems. These systems consist of component 1 (VFe protein, FeFe protein or, MoFe protein respectively) and, component 2 (Fe protein). MoFe is an alpha2beta2 tetramer, V-and Fe- nitrogenases are alpha2beta2delta2 hexamers. The alpha and beta subunits of VFe and FeFe are similar to the alpha and beta subunits of MoFe. For MoFe each alphabeta pair contains one P-cluster (at the alphabeta interface) and, one molecule of iron molybdenum cofactor (FeMoco) contained within the alpha subunit. The Fe p
Probab=22.45 E-value=8.3e+02 Score=24.82 Aligned_cols=178 Identities=13% Similarity=0.115 Sum_probs=89.3
Q ss_pred CcCEEEEcccc-cCC----hHHHHHHHHHhCC----CCCeEEEEeccccHhHHHHHHHHHHhCCCeEE-ecCCC----CC
Q 042576 9 RIPCLYVFVEI-KID----VNRLIDTIKVNYS----DPGKLILAGTIQFASAIRAAKPELEKQGFKVM-IPQSK----PL 74 (313)
Q Consensus 9 ~ipvlYVFv~i-~iD----~~~~i~~i~~~f~----~~~~i~Lv~tiQf~~~l~~~~~~L~~~g~~v~-ipq~~----pl 74 (313)
.+||++|-..- .-+ .+..++++.+.+. ...+|.|++.-.-...+..+++.|+.-|.++. ++... |+
T Consensus 125 ~~~vi~v~tpgF~Gs~~~G~~~a~~ali~~~~~~~~~~~~VNii~~~~~~~D~~ei~~lL~~~Gl~v~~~~d~~~~d~~~ 204 (454)
T cd01973 125 EVHLIPVHTPSFKGSMVTGYDEAVRSVVKTIAKKGAPSGKLNVFTGWVNPGDVVELKHYLSEMDVEANILMDTEDFDSPM 204 (454)
T ss_pred CCeEEEeeCCCcCCCHHHHHHHHHHHHHHHhcccCCCCCcEEEECCCCChHHHHHHHHHHHHcCCCEEEeeccccccCCC
Confidence 46777763311 111 2234444444332 23468888754445678999999999998864 44321 22
Q ss_pred CCc-c--cc-CCCCCCCCCCCCCCeEEEecC--CcccHHHHHhhCCCceEEEeC-CCCCccccccc----------ChHH
Q 042576 75 SAG-E--VL-GCTAPKIPARESDFNLVFIAD--GRFHLEAFMISNPGIKTFRYD-PYLGKLFLEEY----------DNKG 137 (313)
Q Consensus 75 s~G-e--vL-GCt~~~~~~~~~~d~iv~igd--GrFHle~~mi~np~~~~y~yD-Pys~~~~~e~~----------d~~~ 137 (313)
.|. . .- |++...+.+-.+...-+.+++ |. .+-..|=..-+.|.+.++ |+--+-|.+-+ -.++
T Consensus 205 ~~~~~~~~~g~~~~~~i~~~~~A~~niv~~~~~~~-~~A~~Le~~fGiPyi~~~~P~G~~~T~~~l~~ia~~~g~~~~e~ 283 (454)
T cd01973 205 LPDKSAVTHGNTTIEDIADSANAIATIALARYEGG-KAAEFLQKKFDVPAILGPTPIGIKNTDAFLQNIKELTGKPIPES 283 (454)
T ss_pred CCcccccCCCCCCHHHHHHhhhCcEEEEEChhhhH-HHHHHHHHHHCCCeeccCCCcChHHHHHHHHHHHHHHCCCCCHH
Confidence 221 0 01 222222211111333444543 32 222233233356777777 65322211100 1234
Q ss_pred HHHHHHHHHHHHh------hcCCEEEEEEeCCCCCCcHHHHHHHHHHHHHcCCcEEEEEeCCC
Q 042576 138 MRETRKRAIEKAM------KEARTWGIVLGTLGRQGNPRILERLQKRMEKKGFDYVVIMMSEI 194 (313)
Q Consensus 138 ~l~~R~~~I~kak------~~A~~~GIIvgTLg~Q~~~~ii~~l~~ll~~~Gkk~y~i~v~ei 194 (313)
+.+.|..++.... ...+++.|. | .+..+-.+.+.|.+.|.+...++++.-
T Consensus 284 i~~er~~~~~~~~~~~~~~l~Gkrv~i~-g------~~~~~~~l~~fl~elGm~~~~~~~~~~ 339 (454)
T cd01973 284 LVRERGIAIDALADLAHMFFANKKVAIF-G------HPDLVIGLAEFCLEVEMKPVLLLLGDD 339 (454)
T ss_pred HHHHHHHHHHHHHHHHHHHhCCCeEEEE-c------CHHHHHHHHHHHHHCCCeEEEEEECCC
Confidence 4445544443322 135566544 3 346777888888899999888777753
No 280
>cd03825 GT1_wcfI_like This family is most closely related to the GT1 family of glycosyltransferases. wcfI in Bacteroides fragilis has been shown to be involved in the capsular polysaccharide biosynthesis.
Probab=22.43 E-value=2.6e+02 Score=25.57 Aligned_cols=56 Identities=13% Similarity=0.037 Sum_probs=40.7
Q ss_pred EEEEEEeCCCCCCcHHHHHHHHHHHHHcCCcEEEEEeCCCCHHHHhcCcCCccEEEE
Q 042576 155 TWGIVLGTLGRQGNPRILERLQKRMEKKGFDYVVIMMSEISPARVALFEDSVDAWIQ 211 (313)
Q Consensus 155 ~~GIIvgTLg~Q~~~~ii~~l~~ll~~~Gkk~y~i~v~einp~KLanf~~~ID~fV~ 211 (313)
++.++..+.+.-|.-..+..+.+.|.++|.++.++........++.+.. .+|+...
T Consensus 2 kIl~~~~~~~~gG~~~~~~~l~~~l~~~G~~v~v~~~~~~~~~~~~~~~-~~diih~ 57 (365)
T cd03825 2 KVLHLNTSDISGGAARAAYRLHRALQAAGVDSTMLVQEKKALISKIEII-NADIVHL 57 (365)
T ss_pred eEEEEecCCCCCcHHHHHHHHHHHHHhcCCceeEEEeecchhhhChhcc-cCCEEEE
Confidence 3566666666677778888899999999999999988876444444444 4787654
No 281
>TIGR02883 spore_cwlD N-acetylmuramoyl-L-alanine amidase CwlD. Members of this protein family are the CwlD family of N-acetylmuramoyl-L-alanine amidase. This family has been called the germination-specific N-acetylmuramoyl-L-alanine amidase. CwlD is required, along with the putative deactylase PdaA, to make muramic delta-lactam, a novel peptidoglycan constituent found only in spores. CwlD mutants show a germination defect.
Probab=22.38 E-value=1.9e+02 Score=25.46 Aligned_cols=48 Identities=15% Similarity=0.122 Sum_probs=30.6
Q ss_pred CcHHHHHHHHHHHHHcCCcEEEEEeCCCCH-------------------HHHhcCcCCccEEEEecCC
Q 042576 167 GNPRILERLQKRMEKKGFDYVVIMMSEISP-------------------ARVALFEDSVDAWIQIACP 215 (313)
Q Consensus 167 ~~~~ii~~l~~ll~~~Gkk~y~i~v~einp-------------------~KLanf~~~ID~fV~iaCP 215 (313)
-++.+..+|+++|++.|.++++.--+..+. .+++|=. ..|+||-|=|=
T Consensus 27 ~~l~ia~~l~~~L~~~G~~V~ltr~~d~~~~~~~~~~~~~~~~~~L~~R~~~An~~-~adlfiSiH~N 93 (189)
T TIGR02883 27 ITLEIALKLKDYLQEQGALVVMTREDDSDLASEGTKGYSRRKIEDLRKRVKLINES-EADLFISIHLN 93 (189)
T ss_pred HHHHHHHHHHHHHHhCCCEEEEEecCCcCccccccccccccccCCHHHHHHHHHhc-CCCEEEEEecC
Confidence 345667788888888887777655544331 2344433 47888888773
No 282
>PRK03708 ppnK inorganic polyphosphate/ATP-NAD kinase; Provisional
Probab=22.24 E-value=1.7e+02 Score=27.88 Aligned_cols=84 Identities=26% Similarity=0.362 Sum_probs=51.4
Q ss_pred EEEEEEeCCCCCCcHHHHHHHHHHHHHcCCcEEEEEeC--CCCHH---HHhcCc-CCccEEEEec---------------
Q 042576 155 TWGIVLGTLGRQGNPRILERLQKRMEKKGFDYVVIMMS--EISPA---RVALFE-DSVDAWIQIA--------------- 213 (313)
Q Consensus 155 ~~GIIvgTLg~Q~~~~ii~~l~~ll~~~Gkk~y~i~v~--einp~---KLanf~-~~ID~fV~ia--------------- 213 (313)
++||+. ..+.+...+++++|.+.|+++|.++++.... ..... .+.+.. .++|+.|.++
T Consensus 2 ~v~iv~-~~~k~~~~~~~~~I~~~L~~~g~~v~v~~~~~~~~~~~~~~~~~~~~~~~~d~vi~iGGDGTlL~a~~~~~~~ 80 (277)
T PRK03708 2 RFGIVA-RRDKEEALKLAYRVYDFLKVSGYEVVVDSETYEHLPEFSEEDVLPLEEMDVDFIIAIGGDGTILRIEHKTKKD 80 (277)
T ss_pred EEEEEe-cCCCHHHHHHHHHHHHHHHHCCCEEEEecchhhhcCcccccccccccccCCCEEEEEeCcHHHHHHHHhcCCC
Confidence 467774 4467888999999999999999888775311 11100 001111 1477776543
Q ss_pred CCCccccccC-CCCCcccCHHHHHHHhC
Q 042576 214 CPRLSIDWGD-AFTKPLLTPFEAEIALG 240 (313)
Q Consensus 214 CPrlsid~~~-~f~kPvLTPyE~~vAL~ 240 (313)
||=+.|--|. .|.+- +.|.|+.-+|.
T Consensus 81 ~pi~gIn~G~lGFl~~-~~~~~~~~~l~ 107 (277)
T PRK03708 81 IPILGINMGTLGFLTE-VEPEETFFALS 107 (277)
T ss_pred CeEEEEeCCCCCcccc-CCHHHHHHHHH
Confidence 4545554443 57665 45888888874
No 283
>cd06314 PBP1_tmGBP Periplasmic sugar-binding domain of Thermotoga maritima glucose-binding protein (tmGBP) and its close homologs. Periplasmic sugar-binding domain of Thermotoga maritima glucose-binding protein (tmGBP) and its close homologs from other bacteria. They are a member of the type I periplasmic binding protein superfamily which consists of two domains connected by a three-stranded hinge. TmGBP is specific for glucose and its binding pocket is buried at the interface of the two domains. TmGBP also exhibits high thermostability and the highest structural similarity to E. coli glucose binding protein (ecGBP).
Probab=22.13 E-value=2.2e+02 Score=25.45 Aligned_cols=58 Identities=12% Similarity=-0.029 Sum_probs=0.0
Q ss_pred EEEEEEeCCCCCCcHHHHHHHHHHHHHcCCcEEEEEeCCCCHHHHhcC------cCCccEEEEecC
Q 042576 155 TWGIVLGTLGRQGNPRILERLQKRMEKKGFDYVVIMMSEISPARVALF------EDSVDAWIQIAC 214 (313)
Q Consensus 155 ~~GIIvgTLg~Q~~~~ii~~l~~ll~~~Gkk~y~i~v~einp~KLanf------~~~ID~fV~iaC 214 (313)
+||+|+ .+.--....++..+.+.+++.|....++.-+.-++++...+ . .+|++|+.+.
T Consensus 1 ~i~~v~-~~~~~~~~~~~~gi~~~~~~~g~~~~~~~~~~~~~~~~~~~i~~l~~~-~vDgiIi~~~ 64 (271)
T cd06314 1 TIAVVT-NGASPFWKIAEAGVKAAGKELGVDVEFVVPQQGTVNAQLRMLEDLIAE-GVDGIAISPI 64 (271)
T ss_pred CeEEEc-CCCcHHHHHHHHHHHHHHHHcCCeEEEeCCCCCCHHHHHHHHHHHHhc-CCCEEEEecC
No 284
>PRK08745 ribulose-phosphate 3-epimerase; Provisional
Probab=22.09 E-value=4.4e+02 Score=24.28 Aligned_cols=41 Identities=10% Similarity=0.259 Sum_probs=28.8
Q ss_pred HHHHHHHHHHHcCCcEEEEEeCCCCHHHHhcCc-CCccEEEE
Q 042576 171 ILERLQKRMEKKGFDYVVIMMSEISPARVALFE-DSVDAWIQ 211 (313)
Q Consensus 171 ii~~l~~ll~~~Gkk~y~i~v~einp~KLanf~-~~ID~fV~ 211 (313)
-++++++++.++|+++-+-+=|-||.+-+..+. ..+|+||.
T Consensus 157 KI~~l~~~~~~~~~~~~IeVDGGI~~eti~~l~~aGaDi~V~ 198 (223)
T PRK08745 157 KLRAIRKKIDALGKPIRLEIDGGVKADNIGAIAAAGADTFVA 198 (223)
T ss_pred HHHHHHHHHHhcCCCeeEEEECCCCHHHHHHHHHcCCCEEEE
Confidence 344555667777877667777789998887653 14899887
No 285
>PRK13232 nifH nitrogenase reductase; Reviewed
Probab=21.97 E-value=1.6e+02 Score=27.22 Aligned_cols=34 Identities=21% Similarity=0.363 Sum_probs=29.8
Q ss_pred CEEEEEEeCCCCCCcHHHHHHHHHHHHHcCCcEEEE
Q 042576 154 RTWGIVLGTLGRQGNPRILERLQKRMEKKGFDYVVI 189 (313)
Q Consensus 154 ~~~GIIvgTLg~Q~~~~ii~~l~~ll~~~Gkk~y~i 189 (313)
++|+|. | +||-|--.+.-+|--.|.++|+++.++
T Consensus 2 ~~iav~-g-KGGVGKTT~a~nLA~~La~~G~rVllv 35 (273)
T PRK13232 2 RQIAIY-G-KGGIGKSTTTQNLTAALSTMGNKILLV 35 (273)
T ss_pred CEEEEE-C-CCCCcHHHHHHHHHHHHHhhCCCeEEE
Confidence 577888 6 999999999999999999999998776
No 286
>TIGR01501 MthylAspMutase methylaspartate mutase, S subunit. This model represents the S (sigma) subunit of methylaspartate mutase (glutamate mutase), a cobalamin-dependent enzyme that catalyzes the first step in a pathway of glutamate fermentation.
Probab=21.96 E-value=1.9e+02 Score=24.69 Aligned_cols=46 Identities=13% Similarity=0.207 Sum_probs=31.3
Q ss_pred HHHHHhh-cCCEEEEEEeCCCCCCcHHHHHHHHHHHHHcCCcEEEEEeCC
Q 042576 145 AIEKAMK-EARTWGIVLGTLGRQGNPRILERLQKRMEKKGFDYVVIMMSE 193 (313)
Q Consensus 145 ~I~kak~-~A~~~GIIvgTLg~Q~~~~ii~~l~~ll~~~Gkk~y~i~v~e 193 (313)
.++.|++ ++..+| +|+|-+ .....++++.++|+++|..-..+++|-
T Consensus 44 ~v~aa~~~~adiVg--lS~l~~-~~~~~~~~~~~~l~~~gl~~~~vivGG 90 (134)
T TIGR01501 44 FIKAAIETKADAIL--VSSLYG-HGEIDCKGLRQKCDEAGLEGILLYVGG 90 (134)
T ss_pred HHHHHHHcCCCEEE--Eecccc-cCHHHHHHHHHHHHHCCCCCCEEEecC
Confidence 4455551 455555 477776 455567888999999987666677776
No 287
>cd06276 PBP1_FucR_like Ligand-binding domain of a transcription repressor, FucR, which functions as a molecular sensor of L-fucose availability. Ligand-binding domain of a transcription repressor, FucR, which functions as a molecular sensor of L-fucose availability. FcuR acts as an inducer of fucRRIAK and as a corepressor of another locus that regulates production of fucosylated glycans. FcuR and its close homologs in this group are a member of the LacI-GalR family repressors that are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes t
Probab=21.87 E-value=1.6e+02 Score=26.46 Aligned_cols=58 Identities=10% Similarity=0.086 Sum_probs=32.1
Q ss_pred EEEEEeCCCCCCcHHHHHHHHHHHHHcC-CcEEEEEeCCCCHH-HHh-cCcCCccEEEEecCC
Q 042576 156 WGIVLGTLGRQGNPRILERLQKRMEKKG-FDYVVIMMSEISPA-RVA-LFEDSVDAWIQIACP 215 (313)
Q Consensus 156 ~GIIvgTLg~Q~~~~ii~~l~~ll~~~G-kk~y~i~v~einp~-KLa-nf~~~ID~fV~iaCP 215 (313)
+.|+++.+ --.+..++..|.+.++++| ...++...++ ... .+. .....+|.+|++++.
T Consensus 2 ~~~~~~~~-~~~~~~~~~~i~~~l~~~g~~~l~~~~~~~-~~~~~~~~~~~~~vdGvIi~~~~ 62 (247)
T cd06276 2 ILLLLNKL-SSFKEIIYNSFVNTLGKNAQVDLYFHHYNE-DLFKNIISNTKGKYSGYVVMPHF 62 (247)
T ss_pred EEEEEecC-chHHHHHHHHHHHHHHhcCcEEEEEEcCch-HHHHHHHHHHhcCCCEEEEecCC
Confidence 56777777 5566677788888888877 4433333332 111 111 011137887777653
No 288
>PF14157 YmzC: YmzC-like protein; PDB: 3KVP_E.
Probab=21.85 E-value=50 Score=24.84 Aligned_cols=34 Identities=24% Similarity=0.390 Sum_probs=20.7
Q ss_pred CeEEEecCCcccHHHHHhhCCCceEEEeCCCCCcccc
Q 042576 94 FNLVFIADGRFHLEAFMISNPGIKTFRYDPYLGKLFL 130 (313)
Q Consensus 94 d~iv~igdGrFHle~~mi~np~~~~y~yDPys~~~~~ 130 (313)
..++=++.+.|- ++=..-.+++|+|||.+++++.
T Consensus 22 s~m~ql~~N~Fa---v~~e~~~iKIfkyd~~tNei~L 55 (63)
T PF14157_consen 22 SNMTQLEHNHFA---VVDEDGQIKIFKYDEDTNEITL 55 (63)
T ss_dssp EEEEE-STTEEE---EE-ETTEEEEEEEETTTTEEEE
T ss_pred CceEEecCCEEE---EEecCCeEEEEEeCCCCCeEEE
Confidence 344556666653 1112235799999999998764
No 289
>PRK08091 ribulose-phosphate 3-epimerase; Validated
Probab=21.85 E-value=4.3e+02 Score=24.60 Aligned_cols=49 Identities=12% Similarity=0.294 Sum_probs=31.5
Q ss_pred CCCCCcH-HHHHHHH---HHHHHcCCcEEEEEeCCCCHHHHhcCc-CCccEEEE
Q 042576 163 LGRQGNP-RILERLQ---KRMEKKGFDYVVIMMSEISPARVALFE-DSVDAWIQ 211 (313)
Q Consensus 163 Lg~Q~~~-~ii~~l~---~ll~~~Gkk~y~i~v~einp~KLanf~-~~ID~fV~ 211 (313)
.|+|... ..+++++ ++++++|.++.+-+=|-||.+-+.... ..+|+||.
T Consensus 153 fgGQ~f~~~~l~KI~~lr~~~~~~~~~~~IeVDGGI~~~ti~~l~~aGaD~~V~ 206 (228)
T PRK08091 153 TGTKAPSDLILDRVIQVENRLGNRRVEKLISIDGSMTLELASYLKQHQIDWVVS 206 (228)
T ss_pred CCCccccHHHHHHHHHHHHHHHhcCCCceEEEECCCCHHHHHHHHHCCCCEEEE
Confidence 3455544 4455544 566677777666666789988776553 24898876
No 290
>PRK05452 anaerobic nitric oxide reductase flavorubredoxin; Provisional
Probab=21.80 E-value=3.9e+02 Score=27.36 Aligned_cols=79 Identities=4% Similarity=0.055 Sum_probs=53.5
Q ss_pred cCCEEEEEEeCCCCCCcHHHHHHHHHHHHHc--CCcEEEEEeCCCCHHHHh-cCcCCccEEEEecCCCccccccCCCCCc
Q 042576 152 EARTWGIVLGTLGRQGNPRILERLQKRMEKK--GFDYVVIMMSEISPARVA-LFEDSVDAWIQIACPRLSIDWGDAFTKP 228 (313)
Q Consensus 152 ~A~~~GIIvgTLg~Q~~~~ii~~l~~ll~~~--Gkk~y~i~v~einp~KLa-nf~~~ID~fV~iaCPrlsid~~~~f~kP 228 (313)
..+++-||-+|..+ +...+++.|.+-+++. |.++.++-+.+..++.|. .+. +.|+ |+++||=. .+..+. |
T Consensus 250 ~~~kv~IvY~S~~G-nTe~mA~~ia~gl~~~g~gv~v~~~~v~~~~~~~i~~~~~-~ad~-vilGspT~---~~~~~p-~ 322 (479)
T PRK05452 250 QEDRITIFYDTMSN-NTRMMADAIAQGIAEVDPRVAVKIFNVARSDKNEILTNVF-RSKG-VLVGSSTM---NNVMMP-K 322 (479)
T ss_pred CcCcEEEEEECCcc-HHHHHHHHHHHHHHhhCCCceEEEEECCCCCHHHHHhHHh-hCCE-EEEECCcc---CCcchH-H
Confidence 34678899988642 3446889999999987 578888889999998865 344 4675 66777763 222233 5
Q ss_pred ccCHHHHHH
Q 042576 229 LLTPFEAEI 237 (313)
Q Consensus 229 vLTPyE~~v 237 (313)
+...++...
T Consensus 323 ~~~fl~~l~ 331 (479)
T PRK05452 323 IAGLLEEIT 331 (479)
T ss_pred HHHHHHHhh
Confidence 555555543
No 291
>TIGR00829 FRU PTS system, fructose-specific, IIB component. Bacterial PTS transporters transport and concomitantly phosphorylate their sugar substrates, and typically consist of multiple subunits or protein domains. The Fru family is a large and complex family which includes several sequenced fructose and mannitol-specific permeases as well as several PTS components of unknown specificities. The fructose components of this family phosphorylate fructose on the 1-position. The Fru family PTS systems typically have 3 domains, IIA, IIB and IIC, which may be found as 1 or more proteins. The fructose and mannitol transporters form separate phylogenetic clusters in this family. This family is specific for the IIB domain of the fructose PTS transporters.
Probab=21.76 E-value=2.2e+02 Score=22.12 Aligned_cols=68 Identities=22% Similarity=0.254 Sum_probs=43.2
Q ss_pred EEEEeCCCCCCcHHHHHHHHHHHHHcCCcEE------EEEeCCCCHHHHhcCcCCccEEEEecCCCccccccCCCC-Ccc
Q 042576 157 GIVLGTLGRQGNPRILERLQKRMEKKGFDYV------VIMMSEISPARVALFEDSVDAWIQIACPRLSIDWGDAFT-KPL 229 (313)
Q Consensus 157 GIIvgTLg~Q~~~~ii~~l~~ll~~~Gkk~y------~i~v~einp~KLanf~~~ID~fV~iaCPrlsid~~~~f~-kPv 229 (313)
+|.-+.-|.....=..+.|++..++.|.+.. .-+.++++++.++. .|++|.++-.. +|...+|. ||+
T Consensus 2 ~vtacp~G~Aht~lAae~L~~aA~~~G~~i~VE~qg~~g~~~~lt~~~i~~----Ad~viia~d~~--~~~~~rf~gk~v 75 (85)
T TIGR00829 2 AVTACPTGIAHTFMAAEALEKAAKKRGWEVKVETQGSVGAQNALTAEDIAA----ADGVILAADRE--IDLSRRFAGKNV 75 (85)
T ss_pred EEecCCCcHHHHHHHHHHHHHHHHHCCCeEEEEecCCcCccCCCCHHHHHh----CCEEEEeccCC--CchhhhcCCCeE
Confidence 3444444555555566888888888888877 34455677776554 57888888776 45444343 555
Q ss_pred c
Q 042576 230 L 230 (313)
Q Consensus 230 L 230 (313)
+
T Consensus 76 ~ 76 (85)
T TIGR00829 76 Y 76 (85)
T ss_pred E
Confidence 4
No 292
>PF09652 Cas_VVA1548: Putative CRISPR-associated protein (Cas_VVA1548); InterPro: IPR013443 Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) are a family of DNA direct repeats separated by regularly sized non-repetitive spacer sequences that are found in most bacterial and archaeal genomes []. CRISPRs appear to provide acquired resistance against bacteriophages, possibly acting with an RNA interference-like mechanism to inhibit gene functions of invasive DNA elements [, ]. Differences in the number and type of spacers between CRISPR repeats correlate with phage sensitivity. It is thought that following phage infection, bacteria integrate new spacers derived from phage genomic sequences, and that the removal or addition of particular spacers modifies the phage-resistance phenotype of the cell. Therefore, the specificity of CRISPRs may be determined by spacer-phage sequence similarity. In addition, there are many protein families known as CRISPR-associated sequences (Cas), which are encoded in the vicinity of CRISPR loci []. CRISPR/cas gene regions can be quite large, with up to 20 different, tandem-arranged cas genes next to a CRISPR cluster or filling the region between two repeat clusters. Cas genes and CRISPRs are found on mobile genetic elements such as plasmids, and have undergone extensive horizontal transfer. Cas proteins are thought to be involved in the propagation and functioning of CRISPRs. Some Cas proteins show similarity to helicases and repair proteins, although the functions of most are unknown. Cas families can be divided into subtypes according to operon organisation and phylogeny. This entry represents a conserved region of about 95 amino acids found exclusively in species with CRISPR repeats. In all bacterial species that contain this entry, the genes encoding the proteins are in the midst of a cluster of cas genes.
Probab=21.66 E-value=3e+02 Score=22.30 Aligned_cols=49 Identities=22% Similarity=0.414 Sum_probs=35.3
Q ss_pred EEEeCCCCCCcHHHHHHHHHHHHHcCCcEEEEEeC--------CCCHHHHhcCcCCccEEEEecC
Q 042576 158 IVLGTLGRQGNPRILERLQKRMEKKGFDYVVIMMS--------EISPARVALFEDSVDAWIQIAC 214 (313)
Q Consensus 158 IIvgTLg~Q~~~~ii~~l~~ll~~~Gkk~y~i~v~--------einp~KLanf~~~ID~fV~iaC 214 (313)
+|+|||.. +|-..+-++|-++|-+.|. |++.+.|..+...++-|=+.-|
T Consensus 37 ~ViGtLPv--------hLaA~vc~kGa~y~~L~l~lp~e~RG~ELsae~m~~~ga~l~~y~v~~~ 93 (93)
T PF09652_consen 37 VVIGTLPV--------HLAAEVCEKGARYYHLSLDLPAEQRGRELSAEQMRACGARLERYRVHKC 93 (93)
T ss_pred EEEEeCcH--------HHHHHHHhCCcEEEEEEccCChHHcCCcccHHHHHhcCCEEEEEEEEeC
Confidence 78999985 4556666789999999996 7777777777644555544444
No 293
>TIGR02362 dhaK1b probable dihydroxyacetone kinase DhaK1b subunit. Two types of dihydroxyacetone kinase (glycerone kinase) are described. In yeast and a few bacteria, e.g. Citrobacter freundii, the enzyme is a single chain that uses ATP as phosphoryl donor and is designated EC 2.7.1.29. By contract, E. coli and many other bacterial species have a multisubunit form with a phosphoprotein donor related to PTS transport proteins. This family represents a protein, unique to the Firmicutes (low GC Gram-positives), that appears to be a divergent second copy of the K subunit of that complex; its gene is always found in operons with the other three proteins of the complex.
Probab=21.66 E-value=2.6e+02 Score=27.52 Aligned_cols=44 Identities=7% Similarity=0.184 Sum_probs=38.5
Q ss_pred cCCEEEEEEeCCCCCCcHH---HHHHHHHHHHHcCCcEEEEEeCCCC
Q 042576 152 EARTWGIVLGTLGRQGNPR---ILERLQKRMEKKGFDYVVIMMSEIS 195 (313)
Q Consensus 152 ~A~~~GIIvgTLg~Q~~~~---ii~~l~~ll~~~Gkk~y~i~v~ein 195 (313)
+...+.++|+.||+--.++ +.+.+.++|+++|.+.+.+.+|..-
T Consensus 247 ~gd~v~vlvN~LG~t~~lEl~i~~~~v~~~L~~~gi~v~r~~vG~~~ 293 (326)
T TIGR02362 247 ADDHYAVLVNNLGGTTPMEQMVFNNDVHELLALEALHLPFIKVGTFL 293 (326)
T ss_pred CCCEEEEEecCCCCCCHHHHHHHHHHHHHHHHHCCCEEEEeEeeccc
Confidence 5678999999999999987 5788999999999999999888754
No 294
>cd06322 PBP1_ABC_sugar_binding_like_12 Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems. This group includes the periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily, which consist of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis.
Probab=21.45 E-value=1.8e+02 Score=25.71 Aligned_cols=32 Identities=13% Similarity=0.121 Sum_probs=18.9
Q ss_pred EEEEEeCCCCCCcHHHHHHHHHHHHHcCCcEE
Q 042576 156 WGIVLGTLGRQGNPRILERLQKRMEKKGFDYV 187 (313)
Q Consensus 156 ~GIIvgTLg~Q~~~~ii~~l~~ll~~~Gkk~y 187 (313)
+|+|+-+..--.+..+++.+++.+++.|....
T Consensus 2 i~~~~~~~~~~~~~~~~~~i~~~~~~~g~~~~ 33 (267)
T cd06322 2 IGASLLTQQHPFYIELANAMKEEAKKQKVNLI 33 (267)
T ss_pred eeEeecCcccHHHHHHHHHHHHHHHhcCCEEE
Confidence 56666665544555566666666666665443
No 295
>PRK02649 ppnK inorganic polyphosphate/ATP-NAD kinase; Provisional
Probab=21.44 E-value=1.9e+02 Score=27.95 Aligned_cols=36 Identities=28% Similarity=0.424 Sum_probs=28.7
Q ss_pred CEEEEEEeCCCCCCcHHHHHHHHHHHHHcCCcEEEEE
Q 042576 154 RTWGIVLGTLGRQGNPRILERLQKRMEKKGFDYVVIM 190 (313)
Q Consensus 154 ~~~GIIvgTLg~Q~~~~ii~~l~~ll~~~Gkk~y~i~ 190 (313)
+++||+... +.+...+++++|.+.|+++|.++++..
T Consensus 2 ~~igiv~n~-~~~~~~~~~~~l~~~L~~~g~~v~~~~ 37 (305)
T PRK02649 2 PKAGIIYND-GKPLAVRTAEELQDKLEAAGWEVVRAS 37 (305)
T ss_pred CEEEEEEcC-CCHHHHHHHHHHHHHHHHCCCEEEEec
Confidence 468888665 556788899999999999999887643
No 296
>PRK15408 autoinducer 2-binding protein lsrB; Provisional
Probab=21.41 E-value=2.8e+02 Score=26.70 Aligned_cols=63 Identities=16% Similarity=-0.007 Sum_probs=39.0
Q ss_pred cCCEEEEEEeCCCCCCcHHHHHHHHHHHHHcCCcEEEEEeCCCCHHHH----hcC-cCCccEEEEecC
Q 042576 152 EARTWGIVLGTLGRQGNPRILERLQKRMEKKGFDYVVIMMSEISPARV----ALF-EDSVDAWIQIAC 214 (313)
Q Consensus 152 ~A~~~GIIvgTLg~Q~~~~ii~~l~~ll~~~Gkk~y~i~v~einp~KL----anf-~~~ID~fV~iaC 214 (313)
.+++|++|..+++--....+.+-+++.++++|.+..+..-++-++++- .++ ...+|+.|+.+.
T Consensus 22 ~~~~i~~v~k~~~~pf~~~~~~Gi~~aa~~~G~~v~~~~~~~~d~~~q~~~i~~li~~~vdgIiv~~~ 89 (336)
T PRK15408 22 AAERIAFIPKLVGVGFFTSGGNGAKEAGKELGVDVTYDGPTEPSVSGQVQLINNFVNQGYNAIIVSAV 89 (336)
T ss_pred CCcEEEEEECCCCCHHHHHHHHHHHHHHHHhCCEEEEECCCCCCHHHHHHHHHHHHHcCCCEEEEecC
Confidence 466788888777766666777778888888886554322334444432 233 124788777643
No 297
>cd03806 GT1_ALG11_like This family is most closely related to the GT1 family of glycosyltransferases. ALG11 in yeast is involved in adding the final 1,2-linked Man to the Man5GlcNAc2-PP-Dol synthesized on the cytosolic face of the ER. The deletion analysis of ALG11 was shown to block the early steps of core biosynthesis that takes place on the cytoplasmic face of the ER and lead to a defect in the assembly of lipid-linked oligosaccharides.
Probab=21.28 E-value=2e+02 Score=28.39 Aligned_cols=76 Identities=12% Similarity=0.125 Sum_probs=49.3
Q ss_pred EEEEEEeCCCCCCcHHHHHHHHHHHHHcCCcEEEEEeCCCCHHHHhcCcCCccEEEEecCCCccccccCCCCCcccCHHH
Q 042576 155 TWGIVLGTLGRQGNPRILERLQKRMEKKGFDYVVIMMSEISPARVALFEDSVDAWIQIACPRLSIDWGDAFTKPLLTPFE 234 (313)
Q Consensus 155 ~~GIIvgTLg~Q~~~~ii~~l~~ll~~~Gkk~y~i~v~einp~KLanf~~~ID~fV~iaCPrlsid~~~~f~kPvLTPyE 234 (313)
.--+|+|.-.........+.|++++++.|..-.+.+++.++.+.+..+-...|++|..+=. +.|. +++.|
T Consensus 274 ~~lvivG~~~~~~~~~~~~~L~~~~~~l~l~~~V~f~g~v~~~~l~~~l~~adv~v~~s~~-------E~Fg---i~~lE 343 (419)
T cd03806 274 IKLVLIGSCRNEDDEKRVEDLKLLAKELGLEDKVEFVVNAPFEELLEELSTASIGLHTMWN-------EHFG---IGVVE 343 (419)
T ss_pred eEEEEEcCCCCcccHHHHHHHHHHHHHhCCCCeEEEecCCCHHHHHHHHHhCeEEEECCcc-------CCcc---cHHHH
Confidence 4457777633233345778899999998887677788888876666443268998875432 3343 56688
Q ss_pred HHHHhCC
Q 042576 235 AEIALGV 241 (313)
Q Consensus 235 ~~vAL~~ 241 (313)
++ |.|.
T Consensus 344 AM-a~G~ 349 (419)
T cd03806 344 YM-AAGL 349 (419)
T ss_pred HH-HcCC
Confidence 74 4443
No 298
>cd06300 PBP1_ABC_sugar_binding_like_1 Periplasmic sugar-binding component of uncharacterized ABC-type transport systems that are members of the pentose/hexose sugar-binding protein family of the type I periplasmic binding protein superfamily. Periplasmic sugar-binding component of uncharacterized ABC-type transport systems that are members of the pentose/hexose sugar-binding protein family of the type I periplasmic binding protein superfamily, which consists of two alpha/beta globular domains connected by a three-stranded hinge. This Venus flytrap-like domain undergoes transition from an open to a closed conformational state upon ligand binding. Members of this group are predicted to be involved in the transport of sugar-containing molecules across cellular and organellar membranes; however their substrate specificity is not known in detail.
Probab=21.26 E-value=5.8e+02 Score=22.55 Aligned_cols=121 Identities=11% Similarity=0.041 Sum_probs=61.0
Q ss_pred CCCeEEEecCCccc--HHHH-HhhCCCceEEEeCCCCC--cccccccChHHHHH-HHHHHHHHHhhcCCEEEEEEeCCCC
Q 042576 92 SDFNLVFIADGRFH--LEAF-MISNPGIKTFRYDPYLG--KLFLEEYDNKGMRE-TRKRAIEKAMKEARTWGIVLGTLGR 165 (313)
Q Consensus 92 ~~d~iv~igdGrFH--le~~-mi~np~~~~y~yDPys~--~~~~e~~d~~~~l~-~R~~~I~kak~~A~~~GIIvgTLg~ 165 (313)
.+|++++.+... + ...+ .+..-++|++.+|.... .+.....|...+-+ .=..++++.. ..+++++|-|..+.
T Consensus 60 ~vdgiIi~~~~~-~~~~~~l~~~~~~~iPvv~~~~~~~~~~~~~v~~d~~~~g~~~~~~l~~~~~-g~~~i~~i~~~~~~ 137 (272)
T cd06300 60 GVDAIIINPASP-TALNPVIEEACEAGIPVVSFDGTVTTPCAYNVNEDQAEFGKQGAEWLVKELG-GKGNVLVVRGLAGH 137 (272)
T ss_pred CCCEEEEeCCCh-hhhHHHHHHHHHCCCeEEEEecCCCCCceeEecCCHHHHHHHHHHHHHHHcC-CCceEEEEECCCCC
Confidence 378887765321 1 1112 12334678888885421 12222334332211 1122334444 56789999887655
Q ss_pred CCcHHHHHHHHHHHHHcC-CcEEEEEeCCCCHH----HH----hcCcCCccEEEEecCC
Q 042576 166 QGNPRILERLQKRMEKKG-FDYVVIMMSEISPA----RV----ALFEDSVDAWIQIACP 215 (313)
Q Consensus 166 Q~~~~ii~~l~~ll~~~G-kk~y~i~v~einp~----KL----anf~~~ID~fV~iaCP 215 (313)
.....-.+-.++-++++| .+......+.-+.+ .+ ..-+ ++|+++..+..
T Consensus 138 ~~~~~R~~g~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~-~~~~i~~~~d~ 195 (272)
T cd06300 138 PVDEDRYAGAKEVLKEYPGIKIVGEVYGDWDQAVAQKAVADFLASNP-DVDGIWTQGGD 195 (272)
T ss_pred cchHHHHHHHHHHHHHCCCcEEEeecCCCCCHHHHHHHHHHHHHhCC-CcCEEEecCCC
Confidence 444455566777788877 55433333343432 11 2224 57877666555
No 299
>cd01543 PBP1_XylR Ligand-binding domain of DNA transcription repressor specific for xylose (XylR). Ligand-binding domain of DNA transcription repressor specific for xylose (XylR), a member of the LacI-GalR family of bacterial transcription regulators. The ligand-binding domain of XylR is structurally homologous to the periplasmic sugar-binding domain of ABC-type transporters and both domains contain the type I periplasmic binding protein-like fold. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the type I periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.
Probab=21.17 E-value=5.8e+02 Score=22.54 Aligned_cols=127 Identities=11% Similarity=0.069 Sum_probs=62.7
Q ss_pred cccHhHHHHHHHHHHh-CCCeEEecCCCCCCCccccCCCCCCCCCCCCCCeEEEecCCcccHHHHHhhCCCceEEEeCCC
Q 042576 46 IQFASAIRAAKPELEK-QGFKVMIPQSKPLSAGEVLGCTAPKIPARESDFNLVFIADGRFHLEAFMISNPGIKTFRYDPY 124 (313)
Q Consensus 46 iQf~~~l~~~~~~L~~-~g~~v~ipq~~pls~GevLGCt~~~~~~~~~~d~iv~igdGrFHle~~mi~np~~~~y~yDPy 124 (313)
--|...++.+.+.+++ .|+.+++..... ..+-. .+.. ..+|++++.+... -+.. .+..-..|++.+|..
T Consensus 11 ~~~~~~~~gi~~~~~~~~g~~~~~~~~~~------~~~~~-~l~~-~~vdGiI~~~~~~-~~~~-~l~~~~~PvV~~~~~ 80 (265)
T cd01543 11 SYGRGVLRGIARYAREHGPWSIYLEPRGL------QEPLR-WLKD-WQGDGIIARIDDP-EMAE-ALQKLGIPVVDVSGS 80 (265)
T ss_pred hhhHHHHHHHHHHHHhcCCeEEEEecccc------hhhhh-hccc-cccceEEEECCCH-HHHH-HHhhCCCCEEEEeCc
Confidence 3456667888889988 788877643211 01100 0111 2478888764321 1112 123346788888854
Q ss_pred CCc--ccccccChHHHHHHHHHHHH-HHhhcCCEEEEEEeCCCCCCcHHHHHHHHHHHHHcCCcE
Q 042576 125 LGK--LFLEEYDNKGMRETRKRAIE-KAMKEARTWGIVLGTLGRQGNPRILERLQKRMEKKGFDY 186 (313)
Q Consensus 125 s~~--~~~e~~d~~~~l~~R~~~I~-kak~~A~~~GIIvgTLg~Q~~~~ii~~l~~ll~~~Gkk~ 186 (313)
... +.....|..+. -+..+-. ..+ ..++++++ |..+-.....-.+-.++.++++|.+.
T Consensus 81 ~~~~~~~~v~~d~~~~--g~~~~~~l~~~-g~~~i~~i-~~~~~~~~~~R~~gf~~~~~~~~~~~ 141 (265)
T cd01543 81 REKPGIPRVTTDNAAI--GRMAAEHFLER-GFRHFAFY-GLPGARWSDEREEAFRQLVAEAGYEC 141 (265)
T ss_pred cCCCCCCEEeeCHHHH--HHHHHHHHHHC-CCcEEEEE-cCCCCHHHHHHHHHHHHHHHHcCCcc
Confidence 321 22222333222 1211111 123 56788886 54432112233445667788888765
No 300
>PF01915 Glyco_hydro_3_C: Glycosyl hydrolase family 3 C-terminal domain; InterPro: IPR002772 Glycoside hydrolase family 3 GH3 from CAZY comprises enzymes with a number of known activities; beta-glucosidase (3.2.1.21 from EC); beta-xylosidase (3.2.1.37 from EC); N-acetyl beta-glucosaminidase (3.2.1.52 from EC); glucan beta-1,3-glucosidase (3.2.1.58 from EC); cellodextrinase(3.2.1.74 from EC); exo-1,3-1,4-glucanase (3.2.1 from EC). These enzymes are two-domain globular proteins that are N-glycosylated at three sites []. This domain is often C-terminal to the glycoside hydrolase family 3, N-terminal domain IPR001764 from INTERPRO.; GO: 0004553 hydrolase activity, hydrolyzing O-glycosyl compounds, 0005975 carbohydrate metabolic process; PDB: 3LK6_D 3NVD_B 3BMX_B 3ABZ_D 3AC0_D 2X40_A 2X41_A 2X42_A 1J8V_A 1IEX_A ....
Probab=21.12 E-value=2e+02 Score=25.70 Aligned_cols=70 Identities=27% Similarity=0.375 Sum_probs=39.9
Q ss_pred HHHHHhhcCCEEEEEEeCCCCCCc---------------HHHHHHHHHHHHHcCCcEEEEEeCCCCHHHHhcCcCCccEE
Q 042576 145 AIEKAMKEARTWGIVLGTLGRQGN---------------PRILERLQKRMEKKGFDYVVIMMSEISPARVALFEDSVDAW 209 (313)
Q Consensus 145 ~I~kak~~A~~~GIIvgTLg~Q~~---------------~~ii~~l~~ll~~~Gkk~y~i~v~einp~KLanf~~~ID~f 209 (313)
+++.++ +|..+=+.+|+-.+.|. +.--..|-+.+.+.+++.++++ .-=+|--|..|.+++|++
T Consensus 79 ~~~~~~-~aD~vIv~~~~~~~e~~~~~~~~~~~~~~~~l~~~q~~li~~v~~~~~~~Ivvv-~~~~P~~l~~~~~~~~Ai 156 (227)
T PF01915_consen 79 AVAAAK-EADVVIVFVGRPSGEGNDNNTEGESDRSDLALPANQQELIKAVAAAGKKVIVVV-NSGNPYDLDPWEDNVDAI 156 (227)
T ss_dssp HHHHHH-CSSEEEEEEETTSBCCCSS-EETTGSCSSTBCCCHHHHHHHHHHHHHSCEEEEE-E-SSGGCGHCCHHC-SEE
T ss_pred HHHHhh-cCCEEEEeccccccccccccccccCCcccccchhhHHHHHHHHHHhcCCeEEEE-ecCCccccHHHHhhhceE
Confidence 567788 89988888884444442 1122233334445556654433 333555666775469999
Q ss_pred EEecCCC
Q 042576 210 IQIACPR 216 (313)
Q Consensus 210 V~iaCPr 216 (313)
+..--|-
T Consensus 157 l~~~~~g 163 (227)
T PF01915_consen 157 LAAYYPG 163 (227)
T ss_dssp EEEES-G
T ss_pred eeccccc
Confidence 8877766
No 301
>TIGR02955 TMAO_TorT TMAO reductase system periplasmic protein TorT. Members of this family are the periplasmic protein TorT which, together with the the TorS/TorR histidine kinase/response regulator system, regulates expression of the torCAD operon for trimethylamine N-oxide reductase (TMAO reductase). It appears to bind an inducer for TMAO reductase, and shows homology to a periplasmic D-ribose binding protein.
Probab=21.10 E-value=6.4e+02 Score=23.00 Aligned_cols=44 Identities=14% Similarity=0.250 Sum_probs=29.1
Q ss_pred CCEEEEEEeCCCCCCcHHHHHHHHHHHHHcCCcEEEEEeCCCCH
Q 042576 153 ARTWGIVLGTLGRQGNPRILERLQKRMEKKGFDYVVIMMSEISP 196 (313)
Q Consensus 153 A~~~GIIvgTLg~Q~~~~ii~~l~~ll~~~Gkk~y~i~v~einp 196 (313)
.+++++|-|.........-.+-.++-++++|.+...+..+.-++
T Consensus 125 ~~~I~~i~g~~~~~~~~~R~~Gf~~al~~~g~~~~~~~~~~~~~ 168 (295)
T TIGR02955 125 PTTLAWLPGPKNRGGTKPVTQGFRAALEGSDVEISAILWADNDK 168 (295)
T ss_pred CeeEEEEeCCCcCCchhHHHHHHHHHHhcCCcEEEEEecCCCcH
Confidence 45799998887655555556667777887787654444444444
No 302
>PRK10953 cysJ sulfite reductase subunit alpha; Provisional
Probab=20.88 E-value=2.1e+02 Score=30.32 Aligned_cols=51 Identities=10% Similarity=0.124 Sum_probs=42.2
Q ss_pred cCCEEEEEEeCCCCCCcHHHHHHHHHHHHHcCCcEEEEEeCCCCHHHHhcCc
Q 042576 152 EARTWGIVLGTLGRQGNPRILERLQKRMEKKGFDYVVIMMSEISPARVALFE 203 (313)
Q Consensus 152 ~A~~~GIIvgTLg~Q~~~~ii~~l~~ll~~~Gkk~y~i~v~einp~KLanf~ 203 (313)
..+++.|+.||-.| +...+.++|.+.++++|..+-++.|++..++.|....
T Consensus 60 ~~~~v~IlygSqTG-nae~lA~~la~~l~~~g~~~~v~~~~d~~~~~L~~~~ 110 (600)
T PRK10953 60 EMPGITLISASQTG-NARRVAEQLRDDLLAAKLNVNLVNAGDYKFKQIAQEK 110 (600)
T ss_pred CCCeEEEEEEcCch-HHHHHHHHHHHHHHhCCCCcEEechHhCCHhHhccCC
Confidence 56789999999753 3445999999999999999999999999888776554
No 303
>cd02034 CooC The accessory protein CooC, which contains a nucleotide-binding domain (P-loop) near the N-terminus, participates in the maturation of the nickel center of carbon monoxide dehydrogenase (CODH). CODH from Rhodospirillum rubrum catalyzes the reversible oxidation of CO to CO2. CODH contains a nickel-iron-sulfur cluster (C-center) and an iron-sulfur cluster (B-center). CO oxidation occurs at the C-center. Three accessory proteins encoded by cooCTJ genes are involved in nickel incorporation into a nickel site. CooC functions as a nickel insertase that mobilizes nickel to apoCODH using energy released from ATP hydrolysis. CooC is a homodimer and has NTPase activities. Mutation at the P-loop abolishs its function.
Probab=20.82 E-value=2e+02 Score=23.43 Aligned_cols=36 Identities=22% Similarity=0.281 Sum_probs=30.8
Q ss_pred EEEeCCCCCCcHHHHHHHHHHHHHcCCcEEEEEeCC
Q 042576 158 IVLGTLGRQGNPRILERLQKRMEKKGFDYVVIMMSE 193 (313)
Q Consensus 158 IIvgTLg~Q~~~~ii~~l~~ll~~~Gkk~y~i~v~e 193 (313)
|++..+|+.|...+...+...+.++|++..++-.+.
T Consensus 2 i~~~GkgG~GKTt~a~~la~~l~~~g~~V~~id~D~ 37 (116)
T cd02034 2 IAITGKGGVGKTTIAALLARYLAEKGKPVLAIDADP 37 (116)
T ss_pred EEEECCCCCCHHHHHHHHHHHHHHCCCcEEEEECCc
Confidence 677789999999999999999999999877776654
No 304
>TIGR01118 lacA galactose-6-phosphate isomerase, LacA subunit. This family contains members from low GC gram-positive bacteria. Galactose-6-phosphate isomerase is involved in lactose catabolism by the tagatose-6-phosphate pathway.
Probab=20.81 E-value=1.7e+02 Score=25.30 Aligned_cols=80 Identities=16% Similarity=0.197 Sum_probs=44.2
Q ss_pred eEEEEeccccHhHHHHHHHHHHhCCCeEEecCCCCCCCccccCCCCCCCC--------CCCCCCeEEEecCCcccHHHHH
Q 042576 39 KLILAGTIQFASAIRAAKPELEKQGFKVMIPQSKPLSAGEVLGCTAPKIP--------ARESDFNLVFIADGRFHLEAFM 110 (313)
Q Consensus 39 ~i~Lv~tiQf~~~l~~~~~~L~~~g~~v~ipq~~pls~GevLGCt~~~~~--------~~~~~d~iv~igdGrFHle~~m 110 (313)
||++.+|=.=...=+.+++.|++.|++|+= +.+++ .|++|... +.+..-.|++-|.|. +..
T Consensus 2 kI~IgsDh~G~~lK~~i~~~L~~~G~eV~D-----~G~~~--~~dYpd~a~~va~~V~~~e~~~GIliCGtGi----G~s 70 (141)
T TIGR01118 2 AIIIGSDLAGKRLKDVIKNFLVDNGFEVID-----VTEGD--GQDFVDVTLAVASEVQKDEQNLGIVIDAYGA----GSF 70 (141)
T ss_pred EEEEEeCcchHHHHHHHHHHHHHCCCEEEE-----cCCCC--CCCcHHHHHHHHHHHHcCCCceEEEEcCCCH----hHh
Confidence 577777743334446688899999998752 11112 25666421 111234777778884 333
Q ss_pred h-hCCC--c-eEEEeCCCCCccc
Q 042576 111 I-SNPG--I-KTFRYDPYLGKLF 129 (313)
Q Consensus 111 i-~np~--~-~~y~yDPys~~~~ 129 (313)
| +|.- + -+..+|+|+-++.
T Consensus 71 iaANK~~GIRAA~~~d~~~A~~a 93 (141)
T TIGR01118 71 MVATKIKGMIAAEVSDERSAYMT 93 (141)
T ss_pred hhhhcCCCeEEEEECCHHHHHHH
Confidence 3 4422 2 2567777764443
No 305
>cd01481 vWA_collagen_alpha3-VI-like VWA_collagen alpha 3(VI) like: The extracellular matrix represents a complex alloy of variable members of diverse protein families defining structural integrity and various physiological functions. The most abundant family is the collagens with more than 20 different collagen types identified thus far. Collagens are centrally involved in the formation of fibrillar and microfibrillar networks of the extracellular matrix, basement membranes as well as other structures of the extracellular matrix. Some collagens have about 15-18 vWA domains in them. The VWA domains present in these collagens mediate protein-protein interactions.
Probab=20.79 E-value=4.1e+02 Score=22.76 Aligned_cols=49 Identities=12% Similarity=0.167 Sum_probs=35.7
Q ss_pred cCCEEEEEEeCCCCCCcHHHHHHHHHHHHHcCCcEEEEEeCCCCHHHHhcCc
Q 042576 152 EARTWGIVLGTLGRQGNPRILERLQKRMEKKGFDYVVIMMSEISPARVALFE 203 (313)
Q Consensus 152 ~A~~~GIIvgTLg~Q~~~~ii~~l~~ll~~~Gkk~y~i~v~einp~KLanf~ 203 (313)
+++++-||+. =|. ..-. +...-+.|++.|...|.+-++.++.+.|..+.
T Consensus 105 ~~~kv~vviT-dG~-s~d~-~~~~a~~lr~~gv~i~~vG~~~~~~~eL~~ia 153 (165)
T cd01481 105 GVPQFLVLIT-GGK-SQDD-VERPAVALKRAGIVPFAIGARNADLAELQQIA 153 (165)
T ss_pred CCCeEEEEEe-CCC-Ccch-HHHHHHHHHHCCcEEEEEeCCcCCHHHHHHHh
Confidence 4667766664 333 3323 34556788899999999999999999999886
No 306
>PRK09240 thiH thiamine biosynthesis protein ThiH; Reviewed
Probab=20.69 E-value=2.3e+02 Score=27.99 Aligned_cols=57 Identities=21% Similarity=0.092 Sum_probs=38.1
Q ss_pred HHHHHHHHHHHhhcCC----EEEEEEeCCCCCC--cHHHHHHHHHHHHHcCCcEEEEEeCCCCHH
Q 042576 139 RETRKRAIEKAMKEAR----TWGIVLGTLGRQG--NPRILERLQKRMEKKGFDYVVIMMSEISPA 197 (313)
Q Consensus 139 l~~R~~~I~kak~~A~----~~GIIvgTLg~Q~--~~~ii~~l~~ll~~~Gkk~y~i~v~einp~ 197 (313)
...|...|+.|+ +|. ..|+|+|. |..- ...++.+|+.+=...+.--+.|.+.++.|.
T Consensus 201 ~~~rl~~i~~a~-~aG~~~v~~g~i~Gl-ge~~~d~~~~a~~l~~L~~~~~~~~~sv~~~~l~P~ 263 (371)
T PRK09240 201 FEYRLETPERAG-RAGIRKIGLGALLGL-SDWRTDALMTALHLRYLQRKYWQAEYSISFPRLRPC 263 (371)
T ss_pred HHHHHHHHHHHH-HcCCCeeceEEEecC-CccHHHHHHHHHHHHHHHHhCCCCceeeecCccccC
Confidence 567888999999 775 27899884 4322 344566666666566665566777777664
No 307
>cd06309 PBP1_YtfQ_like Periplasmic binding domain of ABC-type YtfQ-like transport systems. Periplasmic binding domain of ABC-type YtfQ-like transport systems. The YtfQ protein from Escherichia coli is up-regulated under glucose-limited conditions and shares homology with a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily. Members of this group are predicted to be involved in the transport of sugar-containing molecules across cellular and organellar membranes; however their ligand specificity is not determined experimentally.
Probab=20.69 E-value=1.9e+02 Score=25.86 Aligned_cols=11 Identities=18% Similarity=0.516 Sum_probs=5.1
Q ss_pred HHcCCcEEEEE
Q 042576 180 EKKGFDYVVIM 190 (313)
Q Consensus 180 ~~~Gkk~y~i~ 190 (313)
...+....++.
T Consensus 52 ~~~~vdgiIi~ 62 (273)
T cd06309 52 IAQGVDVIILA 62 (273)
T ss_pred HHcCCCEEEEc
Confidence 33445555443
No 308
>cd01982 Chlide_reductase_Z Chlide_reductase_Z : Z subunit of chlorophyllide (chlide) reductase (BchZ). Chlide reductase participates in photosynthetic pigment synthesis playing a role in the conversion of chlorophylls(Chl) into bacteriochlorophylls (BChl). Chlide reductase catalyzes the reduction of the B-ring of the tetrapyrolle. Chlide reductase is a three subunit enzyme (subunits are designated BchX, BchY and BchZ). The similarity between these three subunits and the subunits for nitrogenase suggests that BchX serves as an electron donor for the BchY-BchY catalytic subunits.
Probab=20.61 E-value=1.8e+02 Score=29.35 Aligned_cols=74 Identities=12% Similarity=0.157 Sum_probs=52.9
Q ss_pred CCEEEEEEeCCCCCCcHHHHHHHHHHHHHcCCcEEEEEeCCCCHHHHhcCcCCccEEEEecCCCccccccCCCCCc
Q 042576 153 ARTWGIVLGTLGRQGNPRILERLQKRMEKKGFDYVVIMMSEISPARVALFEDSVDAWIQIACPRLSIDWGDAFTKP 228 (313)
Q Consensus 153 A~~~GIIvgTLg~Q~~~~ii~~l~~ll~~~Gkk~y~i~v~einp~KLanf~~~ID~fV~iaCPrlsid~~~~f~kP 228 (313)
..+|-||=.+-+--..+.=++.|+++|+.-|.++..+.-+.-+.+.|.... +-++=+++ |++.+-.-.+.|..|
T Consensus 155 ~~~VNIIG~~~g~~~~~gDl~ElkrLLe~~Gl~vn~v~~~gt~l~eI~~l~-~A~lniv~-~~~~g~~L~e~~giP 228 (412)
T cd01982 155 KGTVNIIGPSYGCFNSPSDLAEVKRLVTGIGAEVNHVYPFESHLAEIPKLK-NAAVNVVM-YREFGRGLAEDLGRP 228 (412)
T ss_pred CCeEEEECCCcCcCCCHHHHHHHHHHHHHcCCcEEEECCCCCCHHHHHhhc-cCCEEEEe-CHHHHHHHHHHHCcC
Confidence 456877755544445577778999999999999998888889999999998 66666665 665332222334444
No 309
>TIGR02836 spore_IV_A stage IV sporulation protein A. A comparative genome analysis of all sequenced genomes of shows a number of proteins conserved strictly among the endospore-forming subset of the Firmicutes. This protein, a member of this panel, is designated stage IV sporulation protein A. It acts in the mother cell compartment and plays a role in spore coat morphogenesis.
Probab=20.54 E-value=2e+02 Score=29.88 Aligned_cols=71 Identities=17% Similarity=0.260 Sum_probs=49.0
Q ss_pred cCCEEEEEEeCCC------CCCcHHHHHHHHHHHHHcCCcEEEEEeCCCCH---H--HH-hcCcCCcc-EEEEecCCCcc
Q 042576 152 EARTWGIVLGTLG------RQGNPRILERLQKRMEKKGFDYVVIMMSEISP---A--RV-ALFEDSVD-AWIQIACPRLS 218 (313)
Q Consensus 152 ~A~~~GIIvgTLg------~Q~~~~ii~~l~~ll~~~Gkk~y~i~v~einp---~--KL-anf~~~ID-~fV~iaCPrls 218 (313)
+-..+||+|.|=| |.++.+.=+++.+.|++.||.+.++ ++...| + .| ..+....+ -++.++|-.+.
T Consensus 143 dhstIgivVtTDgsi~dI~Re~y~~aEe~~i~eLk~~~kPfiiv-lN~~dp~~~et~~l~~~l~eky~vpvl~v~c~~l~ 221 (492)
T TIGR02836 143 EHSTIGVVVTTDGTITDIPREDYVEAEERVIEELKELNKPFIIL-LNSTHPYHPETEALRQELEEKYDVPVLAMDVESMR 221 (492)
T ss_pred hcCcEEEEEEcCCCccccccccchHHHHHHHHHHHhcCCCEEEE-EECcCCCCchhHHHHHHHHHHhCCceEEEEHHHcC
Confidence 4667999999866 5899999999999999999876554 454442 2 11 13321234 35789999987
Q ss_pred ccccC
Q 042576 219 IDWGD 223 (313)
Q Consensus 219 id~~~ 223 (313)
-+|-.
T Consensus 222 ~~DI~ 226 (492)
T TIGR02836 222 ESDIL 226 (492)
T ss_pred HHHHH
Confidence 76644
No 310
>PRK13230 nitrogenase reductase-like protein; Reviewed
Probab=20.53 E-value=1.7e+02 Score=27.08 Aligned_cols=34 Identities=18% Similarity=0.367 Sum_probs=29.0
Q ss_pred CEEEEEEeCCCCCCcHHHHHHHHHHHHHcCCcEEEE
Q 042576 154 RTWGIVLGTLGRQGNPRILERLQKRMEKKGFDYVVI 189 (313)
Q Consensus 154 ~~~GIIvgTLg~Q~~~~ii~~l~~ll~~~Gkk~y~i 189 (313)
++|.|. | +||-|--.+.-+|--.|.++|+++.+|
T Consensus 2 ~~i~~~-g-KGGVGKTT~a~nLA~~La~~G~rVLli 35 (279)
T PRK13230 2 RKFCFY-G-KGGIGKSTTVCNIAAALAESGKKVLVV 35 (279)
T ss_pred cEEEEE-C-CCCCcHHHHHHHHHHHHHhCCCEEEEE
Confidence 567777 6 999999999999999999999986655
No 311
>PRK11557 putative DNA-binding transcriptional regulator; Provisional
Probab=20.47 E-value=3.2e+02 Score=25.22 Aligned_cols=64 Identities=17% Similarity=0.214 Sum_probs=43.8
Q ss_pred HHHHHhhcCCEEEEEEeCCCCCCcHHHHHHHHHHHHHcCCcEEEEEeCCC--CHHHHhcCcCCccEEEEecCCC
Q 042576 145 AIEKAMKEARTWGIVLGTLGRQGNPRILERLQKRMEKKGFDYVVIMMSEI--SPARVALFEDSVDAWIQIACPR 216 (313)
Q Consensus 145 ~I~kak~~A~~~GIIvgTLg~Q~~~~ii~~l~~ll~~~Gkk~y~i~v~ei--np~KLanf~~~ID~fV~iaCPr 216 (313)
+++... +|+++ .|+|. ..+..+.+.+..+|...|+.++.. +.. ...-+.+.. +=|++|.++=++
T Consensus 121 ~~~~i~-~a~~I-~i~G~---G~s~~~A~~~~~~l~~~g~~~~~~--~d~~~~~~~~~~~~-~~Dv~I~iS~sg 186 (278)
T PRK11557 121 CVTMLR-SARRI-ILTGI---GASGLVAQNFAWKLMKIGINAVAE--RDMHALLATVQALS-PDDLLLAISYSG 186 (278)
T ss_pred HHHHHh-cCCeE-EEEec---ChhHHHHHHHHHHHhhCCCeEEEc--CChHHHHHHHHhCC-CCCEEEEEcCCC
Confidence 344446 78886 55554 456778999999999999988753 443 334455676 678888886544
No 312
>cd03795 GT1_like_4 This family is most closely related to the GT1 family of glycosyltransferases. Glycosyltransferases catalyze the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds. The acceptor molecule can be a lipid, a protein, a heterocyclic compound, or another carbohydrate residue. This group of glycosyltransferases is most closely related to the previously defined glycosyltransferase family 1 (GT1). The members of this family may transfer UDP, ADP, GDP, or CMP-linked sugars. The diverse enzymatic activities among members of this family reflect a wide range of biological functions. The protein structure available for this family has the GTB topology, one of the two protein topologies observed for nucleotide-sugar-dependent glycosyltransferases. GTB proteins have distinct N- and C- terminal domains each containing a typical Rossmann fold. The two domains have high structural homology despite minimal sequence homolog
Probab=20.40 E-value=87 Score=28.69 Aligned_cols=44 Identities=11% Similarity=0.100 Sum_probs=32.3
Q ss_pred HHHHHHHHHHcCCcEEEEEeCCCCHHHHhcCcCCccEEEEecCC
Q 042576 172 LERLQKRMEKKGFDYVVIMMSEISPARVALFEDSVDAWIQIACP 215 (313)
Q Consensus 172 i~~l~~ll~~~Gkk~y~i~v~einp~KLanf~~~ID~fV~iaCP 215 (313)
-+.+++++++.+....+.++|.++.+++..+-...|++|+.+-+
T Consensus 230 ~~~~~~~~~~~~~~~~V~~~g~v~~~~~~~~~~~ad~~i~ps~~ 273 (357)
T cd03795 230 EAELEALAAALGLLDRVRFLGRLDDEEKAALLAACDVFVFPSVE 273 (357)
T ss_pred HHHHHHHHHhcCCcceEEEcCCCCHHHHHHHHHhCCEEEeCCcc
Confidence 35667777777777778889999988777654258999886543
No 313
>cd01575 PBP1_GntR Ligand-binding domain of DNA transcription repressor GntR specific for gluconate, a member of the LacI-GalR family of bacterial transcription regulators. This group represents the ligand-binding domain of DNA transcription repressor GntR specific for gluconate, a member of the LacI-GalR family of bacterial transcription regulators. The ligand-binding domain of GntR is structurally homologous to the periplasmic sugar-binding domain of ABC-type transporters and both domains contain the type I periplasmic binding protein-like fold. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the type I periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding,
Probab=20.40 E-value=5.8e+02 Score=22.24 Aligned_cols=158 Identities=16% Similarity=0.190 Sum_probs=72.6
Q ss_pred ccHhHHHHHHHHHHhCCCeEEecCC--CCCCCccccCCCCCCCCCCCCCCeEEEecCCcccHHHH-HhhCCCceEEEeCC
Q 042576 47 QFASAIRAAKPELEKQGFKVMIPQS--KPLSAGEVLGCTAPKIPARESDFNLVFIADGRFHLEAF-MISNPGIKTFRYDP 123 (313)
Q Consensus 47 Qf~~~l~~~~~~L~~~g~~v~ipq~--~pls~GevLGCt~~~~~~~~~~d~iv~igdGrFHle~~-mi~np~~~~y~yDP 123 (313)
-|...++.+.+.+++.|+++++-.. .+...-+.+- .... ..+|++++.+.. .....+ .+..-.+|++.++.
T Consensus 13 ~~~~~~~gi~~~~~~~g~~~~~~~~~~~~~~~~~~~~---~l~~--~~vdgiii~~~~-~~~~~~~~~~~~~ipvv~~~~ 86 (268)
T cd01575 13 VFADVLQGISDVLEAAGYQLLLGNTGYSPEREEELLR---TLLS--RRPAGLILTGLE-HTERTRQLLRAAGIPVVEIMD 86 (268)
T ss_pred hHHHHHHHHHHHHHHcCCEEEEecCCCCchhHHHHHH---HHHH--cCCCEEEEeCCC-CCHHHHHHHHhcCCCEEEEec
Confidence 3555667788888888988765211 1100000000 0001 237888887632 121111 12223567776553
Q ss_pred C--CCcccccccChHHHHHHH-HHHHHHHhhcCCEEEEEEeCCCCCCcHHHHHHHHHHHHHcCCc--EEEEEeCCCCHHH
Q 042576 124 Y--LGKLFLEEYDNKGMRETR-KRAIEKAMKEARTWGIVLGTLGRQGNPRILERLQKRMEKKGFD--YVVIMMSEISPAR 198 (313)
Q Consensus 124 y--s~~~~~e~~d~~~~l~~R-~~~I~kak~~A~~~GIIvgTLg~Q~~~~ii~~l~~ll~~~Gkk--~y~i~v~einp~K 198 (313)
. +........|....-+.= .+++ .+ .-+++|+|-+...-.....-.+-+++.++++|.+ .+.+.....+.++
T Consensus 87 ~~~~~~~~~v~~d~~~~~~~~~~~l~--~~-g~~~i~~i~~~~~~~~~~~r~~gf~~~l~~~~~~~~~~~~~~~~~~~~~ 163 (268)
T cd01575 87 LPPDPIDMAVGFSHAEAGRAMARHLL--AR-GYRRIGFLGARMDDTRAQQRLEGFRAALRAAGLDPPLVVTTPEPSSFAL 163 (268)
T ss_pred CCCCCCCCeEEeCcHHHHHHHHHHHH--HC-CCCcEEEecCCCCcccHHHHHHHHHHHHHHcCCCCCceeEeccCCCHHH
Confidence 2 111111223332221110 0111 23 5578999866543223334456677888888863 3333333333321
Q ss_pred --------HhcCcCCccEEEEecC
Q 042576 199 --------VALFEDSVDAWIQIAC 214 (313)
Q Consensus 199 --------Lanf~~~ID~fV~iaC 214 (313)
|+..+ ++|+++..++
T Consensus 164 ~~~~~~~~l~~~~-~~~ai~~~~d 186 (268)
T cd01575 164 GRELLAELLARWP-DLDAVFCSND 186 (268)
T ss_pred HHHHHHHHHhCCC-CCCEEEECCc
Confidence 22334 5787665443
No 314
>CHL00175 minD septum-site determining protein; Validated
Probab=20.32 E-value=2e+02 Score=26.59 Aligned_cols=41 Identities=12% Similarity=0.180 Sum_probs=33.7
Q ss_pred cCCEEEEEEeCCCCCCcHHHHHHHHHHHHHcCCcEEEEEeC
Q 042576 152 EARTWGIVLGTLGRQGNPRILERLQKRMEKKGFDYVVIMMS 192 (313)
Q Consensus 152 ~A~~~GIIvgTLg~Q~~~~ii~~l~~ll~~~Gkk~y~i~v~ 192 (313)
...++=.|+|++||-|--.+.-+|-..|.+.|+++.+|=++
T Consensus 13 ~~~~vi~v~s~KGGvGKTt~a~nLA~~La~~g~~vlliD~D 53 (281)
T CHL00175 13 TMSRIIVITSGKGGVGKTTTTANLGMSIARLGYRVALIDAD 53 (281)
T ss_pred CCceEEEEEcCCCCCcHHHHHHHHHHHHHhCCCeEEEEeCC
Confidence 34456688899999999999999999999999987666444
No 315
>cd02037 MRP-like MRP (Multiple Resistance and pH adaptation) is a homologue of the Fer4_NifH superfamily. Like the other members of the superfamily, MRP contains a ATP-binding domain at the N-termini. It is found in bacteria as a membrane-spanning protein and functions as a Na+/H+ antiporter.
Probab=20.29 E-value=1.7e+02 Score=24.83 Aligned_cols=35 Identities=17% Similarity=0.276 Sum_probs=29.8
Q ss_pred EEEeCCCCCCcHHHHHHHHHHHHHcCCcEEEEEeC
Q 042576 158 IVLGTLGRQGNPRILERLQKRMEKKGFDYVVIMMS 192 (313)
Q Consensus 158 IIvgTLg~Q~~~~ii~~l~~ll~~~Gkk~y~i~v~ 192 (313)
.+.+.+||.|-..+.-+|-..+.+.|+++.+|=.+
T Consensus 3 ~v~s~kgG~GKTt~a~~LA~~la~~g~~vllvD~D 37 (169)
T cd02037 3 AVMSGKGGVGKSTVAVNLALALAKLGYKVGLLDAD 37 (169)
T ss_pred EEecCCCcCChhHHHHHHHHHHHHcCCcEEEEeCC
Confidence 47889999999999999999999999998887443
No 316
>PF07555 NAGidase: beta-N-acetylglucosaminidase ; InterPro: IPR011496 This family consists of both eukaryotic and prokaryotic hyaluronidases. Human Q9HAR0 from SWISSPROT is expressed during meningioma []. Clostridium perfringens, P26831 from SWISSPROT, is involved in pathogenesis and is likely to act on connectivity tissue during gas gangrene []. It catalyses the random hydrolysis of 1->4-linkages between N-acetyl-beta-D-glucosamine and D-glucuronate residues in hyaluronate.; PDB: 2WB5_B 2V5C_B 2VUR_A 2V5D_A 2YDS_A 2CBI_A 2XPK_A 2CBJ_B 2J62_A 2X0Y_A ....
Probab=20.28 E-value=6.5e+02 Score=24.40 Aligned_cols=88 Identities=18% Similarity=0.278 Sum_probs=47.6
Q ss_pred HHHHHhhCCCceEEEe----CCCCCcccccccChHHHHHHHHHHHHHHhhcCC-EEEEEEe--CCCCCCcHHHHHHHHHH
Q 042576 106 LEAFMISNPGIKTFRY----DPYLGKLFLEEYDNKGMRETRKRAIEKAMKEAR-TWGIVLG--TLGRQGNPRILERLQKR 178 (313)
Q Consensus 106 le~~mi~np~~~~y~y----DPys~~~~~e~~d~~~~l~~R~~~I~kak~~A~-~~GIIvg--TLg~Q~~~~ii~~l~~l 178 (313)
+..+|=.+ ....|.| |||-+.-.+|.|..+++ ..=..+++.|+ ..+ .|+.=++ -.-.-.+.+-++.|+++
T Consensus 20 l~~f~~~~-kmN~YiYAPKdDpyhr~~Wre~Yp~~el-~~l~~L~~~a~-~~~V~Fv~aisPg~~~~~s~~~d~~~L~~K 96 (306)
T PF07555_consen 20 LIRFLGRY-KMNTYIYAPKDDPYHRSKWREPYPEEEL-AELKELADAAK-ANGVDFVYAISPGLDICYSSEEDFEALKAK 96 (306)
T ss_dssp HHHHHHHT-T--EEEE--TT-TTTTTTTTS---HHHH-HHHHHHHHHHH-HTT-EEEEEEBGTTT--TSHHHHHHHHHHH
T ss_pred HHHHHHHc-CCceEEECCCCChHHHhhhcccCCHHHH-HHHHHHHHHHH-HcCCEEEEEECcccccccCcHHHHHHHHHH
Confidence 44444443 5678888 67888888888987765 44456778888 554 3443333 22222234566666665
Q ss_pred HH---HcCCcEEEEEeCCCCH
Q 042576 179 ME---KKGFDYVVIMMSEISP 196 (313)
Q Consensus 179 l~---~~Gkk~y~i~v~einp 196 (313)
+. +.|.+.+-|+++.|..
T Consensus 97 ~~ql~~lGvr~FailfDDi~~ 117 (306)
T PF07555_consen 97 FDQLYDLGVRSFAILFDDIDG 117 (306)
T ss_dssp HHHHHCTT--EEEEE-TS-SS
T ss_pred HHHHHhcCCCEEEEeecCCCC
Confidence 54 4699999999999993
No 317
>PLN02204 diacylglycerol kinase
Probab=20.21 E-value=6.5e+02 Score=27.00 Aligned_cols=64 Identities=16% Similarity=0.190 Sum_probs=46.5
Q ss_pred HHhhcCCEEEEEEeCCCCCCcH-HHHHHHHHHHHHcCCcEEEEEeCCCCHHH-----Hhc--CcCCccEEEEec
Q 042576 148 KAMKEARTWGIVLGTLGRQGNP-RILERLQKRMEKKGFDYVVIMMSEISPAR-----VAL--FEDSVDAWIQIA 213 (313)
Q Consensus 148 kak~~A~~~GIIvgTLg~Q~~~-~ii~~l~~ll~~~Gkk~y~i~v~einp~K-----Lan--f~~~ID~fV~ia 213 (313)
... ..+++-+|+...+++|+- .+.+.+..+++++|.++-+++-..-.-+. ++. .. ..|..|.++
T Consensus 155 ~~~-r~k~llVivNP~sGkg~~~~~~~~V~p~f~~a~i~~~v~~T~~aghA~d~~~~~~~~~l~-~~D~VVaVG 226 (601)
T PLN02204 155 EVG-RPKNLLVFVHPLSGKGSGSRTWETVSPIFIRAKVKTKVIVTERAGHAFDVMASISNKELK-SYDGVIAVG 226 (601)
T ss_pred ccC-CCceEEEEECCCCCCcchHHHHHHHHHHHHHcCCeEEEEEecCcchHHHHHHHHhhhhcc-CCCEEEEEc
Confidence 344 678999999999998874 58889999999999998777777665432 222 23 467766554
No 318
>PRK11468 dihydroxyacetone kinase subunit DhaK; Provisional
Probab=20.16 E-value=2.4e+02 Score=28.19 Aligned_cols=45 Identities=16% Similarity=0.228 Sum_probs=38.9
Q ss_pred cCCEEEEEEeCCCCCCcHH---HHHHHHHHHHHcCCcEEEEEeCCCCH
Q 042576 152 EARTWGIVLGTLGRQGNPR---ILERLQKRMEKKGFDYVVIMMSEISP 196 (313)
Q Consensus 152 ~A~~~GIIvgTLg~Q~~~~---ii~~l~~ll~~~Gkk~y~i~v~einp 196 (313)
+...+.++|+.||+.-.++ +.+++.++|+++|.+.+..++|..-.
T Consensus 274 ~gd~v~vLVNgLG~t~~~El~i~~~~v~~~L~~~gi~v~r~~vG~~~T 321 (356)
T PRK11468 274 SGDRVIALVNNLGATPLSELYGVYNRLATRCEQAGLTIERNLIGAYCT 321 (356)
T ss_pred CCCeEEEEEeCCCCCCHHHHHHHHHHHHHHHHHCCCEEEEeeeecccc
Confidence 5568999999999999998 57889999999999999998887543
No 319
>PF08475 Baculo_VP91_N: Viral capsid protein 91 N-terminal; InterPro: IPR013682 This domain is found in Baculoviridae including the nucleopolyhedrovirus at the N terminus of the viral capsid protein 91 (VP91) [].
Probab=20.10 E-value=89 Score=28.31 Aligned_cols=19 Identities=11% Similarity=0.212 Sum_probs=14.5
Q ss_pred cccHhHHHHHHHHHHhCCC
Q 042576 46 IQFASAIRAAKPELEKQGF 64 (313)
Q Consensus 46 iQf~~~l~~~~~~L~~~g~ 64 (313)
-.|...++-+.+.|+.-+-
T Consensus 26 ~~F~~rL~Vl~EYlkrtna 44 (183)
T PF08475_consen 26 NEFDNRLQVLTEYLKRTNA 44 (183)
T ss_pred HHHHHHHHHHHHHHHhcCC
Confidence 3688888888888887543
No 320
>TIGR01278 DPOR_BchB light-independent protochlorophyllide reductase, B subunit. This enzyme describes the B subunit of the dark form protochlorophyllide reductase, a nitrogenase-like enzyme. This subunit shows homology to the nitrogenase molybdenum-iron protein. It catalyzes a step in bacteriochlorophyll biosynthesis.
Probab=20.08 E-value=2.1e+02 Score=29.46 Aligned_cols=76 Identities=17% Similarity=0.227 Sum_probs=53.2
Q ss_pred cCCEEEEEEeCCCCCCcHHHHHHHHHHHHHcCCcEEEEEeCCCCHHHHhcCcCCccEEEEec-CCCcccc----ccCCCC
Q 042576 152 EARTWGIVLGTLGRQGNPRILERLQKRMEKKGFDYVVIMMSEISPARVALFEDSVDAWIQIA-CPRLSID----WGDAFT 226 (313)
Q Consensus 152 ~A~~~GIIvgTLg~Q~~~~ii~~l~~ll~~~Gkk~y~i~v~einp~KLanf~~~ID~fV~ia-CPrlsid----~~~~f~ 226 (313)
...++-||=.+-.+-..+.=++.|+++|+..|.++-.++-+.-+.+.|.+.+ +++++|. ||+.... -.+.|-
T Consensus 157 ~~~~VNIiG~~~l~~~~~~D~~elkrlL~~lGi~vn~v~p~g~s~~dl~~l~---~A~~NIv~~~~~g~~~A~~Le~~fG 233 (511)
T TIGR01278 157 EKPSVNLLGPASLGFHHRHDLIELRRLLKTLGIEVNVVAPWGASIADLARLP---AAWLNICPYREIGLMAAEYLKEKFG 233 (511)
T ss_pred CCCcEEEEeCCCCCCCCHHHHHHHHHHHHHCCCeEEEEeCCCCCHHHHHhcc---cCcEEEEechHHHHHHHHHHHHHhC
Confidence 3456766654433333455567899999999999988888888999999998 4555554 9885432 235677
Q ss_pred Cccc
Q 042576 227 KPLL 230 (313)
Q Consensus 227 kPvL 230 (313)
.|.+
T Consensus 234 iP~i 237 (511)
T TIGR01278 234 QPYI 237 (511)
T ss_pred CCcc
Confidence 8876
No 321
>COG0761 lytB 4-Hydroxy-3-methylbut-2-enyl diphosphate reductase IspH [Lipid metabolism]
Probab=20.08 E-value=8.2e+02 Score=23.85 Aligned_cols=57 Identities=23% Similarity=0.310 Sum_probs=37.5
Q ss_pred HHHHHHHHHHhhcCCEEEEEEeCCCCCCcHHHHHHHHHHHHHcCCcEEEEE-eCCCCHHHHhc
Q 042576 140 ETRKRAIEKAMKEARTWGIVLGTLGRQGNPRILERLQKRMEKKGFDYVVIM-MSEISPARVAL 201 (313)
Q Consensus 140 ~~R~~~I~kak~~A~~~GIIvgTLg~Q~~~~ii~~l~~ll~~~Gkk~y~i~-v~einp~KLan 201 (313)
..|..++......+. +-||||..-..++. ||.++.+++|.++|++= ..+|.++-|..
T Consensus 200 ~nRQ~Avk~la~~~D-l~iVVG~~nSSNs~----rL~eiA~~~g~~aylId~~~ei~~~w~~~ 257 (294)
T COG0761 200 QNRQDAVKELAPEVD-LVIVVGSKNSSNSN----RLAEIAKRHGKPAYLIDDAEEIDPEWLKG 257 (294)
T ss_pred hhHHHHHHHHhhcCC-EEEEECCCCCccHH----HHHHHHHHhCCCeEEeCChHhCCHHHhcC
Confidence 345556655441444 55999987766664 67888899999988874 34666665544
No 322
>PRK15427 colanic acid biosynthesis glycosyltransferase WcaL; Provisional
Probab=20.02 E-value=91 Score=30.74 Aligned_cols=44 Identities=20% Similarity=0.206 Sum_probs=34.7
Q ss_pred HHHHHHHHHHcCCcEEEEEeCCCCHHHHhcCcCCccEEEEecCC
Q 042576 172 LERLQKRMEKKGFDYVVIMMSEISPARVALFEDSVDAWIQIACP 215 (313)
Q Consensus 172 i~~l~~ll~~~Gkk~y~i~v~einp~KLanf~~~ID~fV~iaCP 215 (313)
.+.+++++++.|..-.+.++|.++.+.+..+-...|+||+-+..
T Consensus 265 ~~~l~~~~~~~~l~~~V~~~G~~~~~el~~~l~~aDv~v~pS~~ 308 (406)
T PRK15427 265 ERRLRTLIEQYQLEDVVEMPGFKPSHEVKAMLDDADVFLLPSVT 308 (406)
T ss_pred HHHHHHHHHHcCCCCeEEEeCCCCHHHHHHHHHhCCEEEECCcc
Confidence 46788899998987788888999877776553379999987765
Done!